Starting phenix.real_space_refine on Mon Aug 25 22:35:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ssa_40749/08_2025/8ssa_40749.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ssa_40749/08_2025/8ssa_40749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ssa_40749/08_2025/8ssa_40749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ssa_40749/08_2025/8ssa_40749.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ssa_40749/08_2025/8ssa_40749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ssa_40749/08_2025/8ssa_40749.map" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 168 5.16 5 C 20007 2.51 5 N 4985 2.21 5 O 5716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30888 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7759 Classifications: {'peptide': 986} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 959} Chain breaks: 4 Chain: "B" Number of atoms: 6238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6238 Classifications: {'peptide': 792} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 768} Chain breaks: 1 Chain: "C" Number of atoms: 7759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7759 Classifications: {'peptide': 986} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 959} Chain breaks: 4 Chain: "D" Number of atoms: 6238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6238 Classifications: {'peptide': 792} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 768} Chain breaks: 1 Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "F" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "A" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 184 Unusual residues: {'PCW': 4} Inner-chain residues flagged as termini: ['pdbres="GLU A1104 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 92 Unusual residues: {'PCW': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 184 Unusual residues: {'PCW': 4} Inner-chain residues flagged as termini: ['pdbres="GLU C1104 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 102 Unusual residues: {'PCW': 2, 'SPD': 1} Inner-chain residues flagged as termini: ['pdbres="GLU D1103 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 8.10, per 1000 atoms: 0.26 Number of scatterers: 30888 At special positions: 0 Unit cell: (118.69, 145.25, 194.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 12 15.00 O 5716 8.00 N 4985 7.00 C 20007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.02 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.02 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.04 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 1.2 microseconds 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7088 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 32 sheets defined 50.9% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 removed outlier: 3.588A pdb=" N GLY A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 68 Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 117 through 128 removed outlier: 3.550A pdb=" N ILE A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 removed outlier: 3.693A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 186 removed outlier: 3.554A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.532A pdb=" N ASP A 203 " --> pdb=" O ASP A 199 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.925A pdb=" N GLY A 230 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.042A pdb=" N PHE A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.518A pdb=" N ARG A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 302 removed outlier: 3.651A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 296 " --> pdb=" O MET A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 334 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.907A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR A 421 " --> pdb=" O ASN A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 421' Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.617A pdb=" N GLY A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 482 through 489 removed outlier: 3.698A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 544 removed outlier: 3.559A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 585 removed outlier: 3.751A pdb=" N PHE A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 624 removed outlier: 4.039A pdb=" N ILE A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 610 " --> pdb=" O TRP A 606 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 618 " --> pdb=" O SER A 614 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 621 " --> pdb=" O THR A 617 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.559A pdb=" N LYS A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 removed outlier: 3.715A pdb=" N GLU A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 676 removed outlier: 3.669A pdb=" N LYS A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.808A pdb=" N ALA A 691 " --> pdb=" O ALA A 687 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.826A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.560A pdb=" N VAL A 746 " --> pdb=" O LEU A 742 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 766 removed outlier: 3.656A pdb=" N TRP A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 780 removed outlier: 3.535A pdb=" N GLY A 779 " --> pdb=" O LYS A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 820 removed outlier: 3.857A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 858 removed outlier: 3.641A pdb=" N SER A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 851 " --> pdb=" O CYS A 847 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 929 removed outlier: 3.516A pdb=" N MET A 924 " --> pdb=" O ASN A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 951 removed outlier: 3.791A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 991 removed outlier: 3.886A pdb=" N SER A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 967 " --> pdb=" O GLY A 963 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1032 removed outlier: 3.851A pdb=" N ILE A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER A1013 " --> pdb=" O PHE A1009 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL A1025 " --> pdb=" O GLY A1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 removed outlier: 3.718A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 81 through 93 removed outlier: 3.659A pdb=" N SER B 87 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.708A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 removed outlier: 3.836A pdb=" N ALA B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 187 removed outlier: 3.525A pdb=" N ARG B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 removed outlier: 4.317A pdb=" N ASP B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 4.176A pdb=" N GLY B 230 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.645A pdb=" N ARG B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 302 removed outlier: 3.572A pdb=" N LEU B 284 " --> pdb=" O TYR B 280 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 300 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.915A pdb=" N GLU B 328 " --> pdb=" O GLY B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 423 through 433 removed outlier: 3.875A pdb=" N ALA B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.951A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B 519 " --> pdb=" O SER B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 515 through 519' Processing helix chain 'B' and resid 524 through 546 removed outlier: 4.163A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 4.042A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 624 removed outlier: 4.205A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY B 602 " --> pdb=" O GLY B 598 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE B 608 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA B 618 " --> pdb=" O SER B 614 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 642 Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.862A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.636A pdb=" N MET B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 705 through 713 removed outlier: 3.588A pdb=" N ASN B 709 " --> pdb=" O GLU B 705 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 755 removed outlier: 3.600A pdb=" N ALA B 749 " --> pdb=" O PRO B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 792 through 819 removed outlier: 3.983A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 805 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 removed outlier: 3.589A pdb=" N GLY C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 68 Processing helix chain 'C' and resid 81 through 93 Processing helix chain 'C' and resid 117 through 128 removed outlier: 3.549A pdb=" N ILE C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 157 removed outlier: 3.692A pdb=" N ALA C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 186 removed outlier: 3.554A pdb=" N ARG C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 removed outlier: 3.531A pdb=" N ASP C 203 " --> pdb=" O ASP C 199 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE C 209 " --> pdb=" O VAL C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.926A pdb=" N GLY C 230 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 4.042A pdb=" N PHE C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.519A pdb=" N ARG C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 302 removed outlier: 3.652A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 334 Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.907A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG C 420 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR C 421 " --> pdb=" O ASN C 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 421' Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.617A pdb=" N GLY C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 467 Processing helix chain 'C' and resid 482 through 489 removed outlier: 3.697A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 544 removed outlier: 3.559A pdb=" N TRP C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 585 removed outlier: 3.751A pdb=" N PHE C 579 " --> pdb=" O ASN C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 624 removed outlier: 4.040A pdb=" N ILE C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY C 602 " --> pdb=" O GLY C 598 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 610 " --> pdb=" O TRP C 606 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C 618 " --> pdb=" O SER C 614 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 621 " --> pdb=" O THR C 617 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 624 " --> pdb=" O LEU C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.560A pdb=" N LYS C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.714A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 676 removed outlier: 3.668A pdb=" N LYS C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 697 removed outlier: 3.808A pdb=" N ALA C 691 " --> pdb=" O ALA C 687 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS C 697 " --> pdb=" O VAL C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.827A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.560A pdb=" N VAL C 746 " --> pdb=" O LEU C 742 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 766 removed outlier: 3.656A pdb=" N TRP C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 780 removed outlier: 3.536A pdb=" N GLY C 779 " --> pdb=" O LYS C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 820 removed outlier: 3.857A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 814 " --> pdb=" O ALA C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 858 removed outlier: 3.640A pdb=" N SER C 842 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 845 " --> pdb=" O SER C 841 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY C 850 " --> pdb=" O VAL C 846 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 851 " --> pdb=" O CYS C 847 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 852 " --> pdb=" O GLY C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 929 removed outlier: 3.516A pdb=" N MET C 924 " --> pdb=" O ASN C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 951 removed outlier: 3.791A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 991 removed outlier: 3.886A pdb=" N SER C 962 " --> pdb=" O LEU C 958 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 967 " --> pdb=" O GLY C 963 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1032 removed outlier: 3.850A pdb=" N ILE C1012 " --> pdb=" O ALA C1008 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER C1013 " --> pdb=" O PHE C1009 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL C1025 " --> pdb=" O GLY C1021 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 removed outlier: 3.717A pdb=" N GLY D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 68 Processing helix chain 'D' and resid 81 through 93 removed outlier: 3.659A pdb=" N SER D 87 " --> pdb=" O ASN D 83 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 removed outlier: 3.709A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 156 removed outlier: 3.837A pdb=" N ALA D 153 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 187 removed outlier: 3.525A pdb=" N ARG D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 removed outlier: 4.318A pdb=" N ASP D 203 " --> pdb=" O ASP D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 230 removed outlier: 4.175A pdb=" N GLY D 230 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.644A pdb=" N ARG D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 302 removed outlier: 3.572A pdb=" N LEU D 284 " --> pdb=" O TYR D 280 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG D 300 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 removed outlier: 3.915A pdb=" N GLU D 328 " --> pdb=" O GLY D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 414 Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 423 through 433 removed outlier: 3.875A pdb=" N ALA D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.951A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP D 519 " --> pdb=" O SER D 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 515 through 519' Processing helix chain 'D' and resid 524 through 546 removed outlier: 4.162A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL D 539 " --> pdb=" O GLY D 535 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE D 541 " --> pdb=" O SER D 537 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 4.041A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 624 removed outlier: 4.204A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY D 602 " --> pdb=" O GLY D 598 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE D 608 " --> pdb=" O VAL D 604 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE D 613 " --> pdb=" O THR D 609 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA D 618 " --> pdb=" O SER D 614 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D 624 " --> pdb=" O LEU D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.862A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.636A pdb=" N MET D 670 " --> pdb=" O VAL D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 697 Processing helix chain 'D' and resid 705 through 713 removed outlier: 3.590A pdb=" N ASN D 709 " --> pdb=" O GLU D 705 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 755 removed outlier: 3.601A pdb=" N ALA D 749 " --> pdb=" O PRO D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 792 through 819 removed outlier: 3.983A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 805 " --> pdb=" O GLY D 801 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 24 removed outlier: 3.587A pdb=" N THR E 13 " --> pdb=" O CYS E 9 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU E 14 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL E 15 " --> pdb=" O MET E 11 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 36 removed outlier: 3.840A pdb=" N ILE E 28 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA E 30 " --> pdb=" O TRP E 26 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE E 31 " --> pdb=" O HIS E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 65 Processing helix chain 'E' and resid 68 through 85 removed outlier: 4.386A pdb=" N HIS E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N CYS E 79 " --> pdb=" O HIS E 75 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU E 80 " --> pdb=" O GLY E 76 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 93 removed outlier: 3.546A pdb=" N GLY E 92 " --> pdb=" O TRP E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 107 removed outlier: 4.321A pdb=" N HIS E 107 " --> pdb=" O TRP E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 111 removed outlier: 3.915A pdb=" N ASP E 111 " --> pdb=" O ARG E 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 108 through 111' Processing helix chain 'E' and resid 126 through 158 removed outlier: 3.542A pdb=" N TYR E 130 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA E 140 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL E 158 " --> pdb=" O VAL E 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 24 removed outlier: 3.584A pdb=" N THR F 13 " --> pdb=" O CYS F 9 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU F 14 " --> pdb=" O TYR F 10 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL F 15 " --> pdb=" O MET F 11 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 36 removed outlier: 3.856A pdb=" N ILE F 28 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA F 30 " --> pdb=" O TRP F 26 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE F 31 " --> pdb=" O HIS F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 65 Processing helix chain 'F' and resid 68 through 85 removed outlier: 4.362A pdb=" N HIS F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE F 78 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS F 79 " --> pdb=" O HIS F 75 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU F 80 " --> pdb=" O GLY F 76 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 93 removed outlier: 3.646A pdb=" N GLY F 92 " --> pdb=" O TRP F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 107 removed outlier: 4.305A pdb=" N HIS F 107 " --> pdb=" O TRP F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 111 removed outlier: 3.923A pdb=" N ASP F 111 " --> pdb=" O ARG F 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 108 through 111' Processing helix chain 'F' and resid 126 through 158 removed outlier: 3.521A pdb=" N TYR F 130 " --> pdb=" O ASP F 126 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP F 136 " --> pdb=" O GLN F 132 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA F 140 " --> pdb=" O TRP F 136 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU F 144 " --> pdb=" O ALA F 140 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL F 158 " --> pdb=" O VAL F 154 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 5.770A pdb=" N ILE A 12 " --> pdb=" O THR A 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.541A pdb=" N GLY A 16 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU A 50 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N PHE A 18 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 164 removed outlier: 7.558A pdb=" N PHE A 133 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE A 163 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TYR A 135 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 193 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 340 removed outlier: 3.685A pdb=" N VAL A 338 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 363 removed outlier: 3.805A pdb=" N GLY A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 395 through 399 removed outlier: 7.203A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 490 through 491 Processing sheet with id=AA8, first strand: chain 'A' and resid 496 through 497 removed outlier: 4.279A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 732 " --> pdb=" O MET A 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 646 through 649 removed outlier: 6.032A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 50 removed outlier: 5.702A pdb=" N GLY B 15 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 164 removed outlier: 8.134A pdb=" N ASP B 195 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU B 136 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 243 through 246 removed outlier: 4.277A pdb=" N GLY B 244 " --> pdb=" O MET B 361 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET B 361 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 337 through 339 removed outlier: 3.929A pdb=" N VAL B 338 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 345 " --> pdb=" O VAL B 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'B' and resid 497 through 498 Processing sheet with id=AB7, first strand: chain 'B' and resid 502 through 505 removed outlier: 4.129A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 11 through 13 removed outlier: 5.770A pdb=" N ILE C 12 " --> pdb=" O THR C 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 47 through 50 removed outlier: 6.541A pdb=" N GLY C 16 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU C 50 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N PHE C 18 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 159 through 164 removed outlier: 7.557A pdb=" N PHE C 133 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE C 163 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TYR C 135 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 193 " --> pdb=" O ALA C 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 337 through 340 removed outlier: 3.686A pdb=" N VAL C 338 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 357 through 363 removed outlier: 3.805A pdb=" N GLY C 372 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 395 through 399 removed outlier: 7.203A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AC6, first strand: chain 'C' and resid 496 through 497 removed outlier: 4.278A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR C 732 " --> pdb=" O MET C 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 646 through 649 removed outlier: 6.032A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 45 through 50 removed outlier: 5.702A pdb=" N GLY D 15 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 159 through 164 removed outlier: 8.133A pdb=" N ASP D 195 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU D 136 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 243 through 246 removed outlier: 4.278A pdb=" N GLY D 244 " --> pdb=" O MET D 361 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET D 361 " --> pdb=" O GLY D 244 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 337 through 339 removed outlier: 3.929A pdb=" N VAL D 338 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 345 " --> pdb=" O VAL D 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AD4, first strand: chain 'D' and resid 497 through 498 Processing sheet with id=AD5, first strand: chain 'D' and resid 502 through 505 removed outlier: 4.129A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) 1236 hydrogen bonds defined for protein. 3612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.22 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5004 1.31 - 1.44: 8592 1.44 - 1.57: 17645 1.57 - 1.69: 26 1.69 - 1.82: 268 Bond restraints: 31535 Sorted by residual: bond pdb=" C31 PCW C1101 " pdb=" O2 PCW C1101 " ideal model delta sigma weight residual 1.333 1.423 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C11 PCW A1103 " pdb=" O3 PCW A1103 " ideal model delta sigma weight residual 1.326 1.416 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C31 PCW A1101 " pdb=" O2 PCW A1101 " ideal model delta sigma weight residual 1.333 1.422 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C11 PCW C1103 " pdb=" O3 PCW C1103 " ideal model delta sigma weight residual 1.326 1.415 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C31 PCW D1102 " pdb=" O2 PCW D1102 " ideal model delta sigma weight residual 1.333 1.421 -0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 31530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 40894 2.91 - 5.82: 1292 5.82 - 8.74: 259 8.74 - 11.65: 66 11.65 - 14.56: 23 Bond angle restraints: 42534 Sorted by residual: angle pdb=" C THR B 383 " pdb=" N GLU B 384 " pdb=" CA GLU B 384 " ideal model delta sigma weight residual 121.54 136.10 -14.56 1.91e+00 2.74e-01 5.81e+01 angle pdb=" C THR D 383 " pdb=" N GLU D 384 " pdb=" CA GLU D 384 " ideal model delta sigma weight residual 121.54 136.10 -14.56 1.91e+00 2.74e-01 5.81e+01 angle pdb=" N THR B 383 " pdb=" CA THR B 383 " pdb=" C THR B 383 " ideal model delta sigma weight residual 110.53 102.54 7.99 1.29e+00 6.01e-01 3.84e+01 angle pdb=" N THR D 383 " pdb=" CA THR D 383 " pdb=" C THR D 383 " ideal model delta sigma weight residual 110.53 102.55 7.98 1.29e+00 6.01e-01 3.83e+01 angle pdb=" C ASP A 378 " pdb=" N LYS A 379 " pdb=" CA LYS A 379 " ideal model delta sigma weight residual 121.54 132.73 -11.19 1.91e+00 2.74e-01 3.43e+01 ... (remaining 42529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 18350 35.38 - 70.77: 362 70.77 - 106.15: 37 106.15 - 141.53: 6 141.53 - 176.92: 10 Dihedral angle restraints: 18765 sinusoidal: 7683 harmonic: 11082 Sorted by residual: dihedral pdb=" CA SER A 403 " pdb=" C SER A 403 " pdb=" N PRO A 404 " pdb=" CA PRO A 404 " ideal model delta harmonic sigma weight residual -180.00 -120.26 -59.74 0 5.00e+00 4.00e-02 1.43e+02 dihedral pdb=" CA SER C 403 " pdb=" C SER C 403 " pdb=" N PRO C 404 " pdb=" CA PRO C 404 " ideal model delta harmonic sigma weight residual 180.00 -120.27 -59.73 0 5.00e+00 4.00e-02 1.43e+02 dihedral pdb=" CA SER D 403 " pdb=" C SER D 403 " pdb=" N PRO D 404 " pdb=" CA PRO D 404 " ideal model delta harmonic sigma weight residual -180.00 -125.12 -54.88 0 5.00e+00 4.00e-02 1.20e+02 ... (remaining 18762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3617 0.070 - 0.140: 931 0.140 - 0.210: 107 0.210 - 0.280: 21 0.280 - 0.350: 6 Chirality restraints: 4682 Sorted by residual: chirality pdb=" CB VAL B 395 " pdb=" CA VAL B 395 " pdb=" CG1 VAL B 395 " pdb=" CG2 VAL B 395 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CB VAL D 395 " pdb=" CA VAL D 395 " pdb=" CG1 VAL D 395 " pdb=" CG2 VAL D 395 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB ILE D 459 " pdb=" CA ILE D 459 " pdb=" CG1 ILE D 459 " pdb=" CG2 ILE D 459 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 4679 not shown) Planarity restraints: 5306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 716 " 0.089 5.00e-02 4.00e+02 1.35e-01 2.93e+01 pdb=" N PRO D 717 " -0.234 5.00e-02 4.00e+02 pdb=" CA PRO D 717 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO D 717 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 716 " -0.089 5.00e-02 4.00e+02 1.35e-01 2.92e+01 pdb=" N PRO B 717 " 0.234 5.00e-02 4.00e+02 pdb=" CA PRO B 717 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 717 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 403 " 0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO B 404 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 404 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 404 " 0.048 5.00e-02 4.00e+02 ... (remaining 5303 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4641 2.75 - 3.29: 30159 3.29 - 3.83: 52392 3.83 - 4.36: 62131 4.36 - 4.90: 101578 Nonbonded interactions: 250901 Sorted by model distance: nonbonded pdb=" OH TYR D 128 " pdb=" OG SER D 243 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR B 128 " pdb=" OG SER B 243 " model vdw 2.213 3.040 nonbonded pdb=" O ASP D 490 " pdb=" OG1 THR D 736 " model vdw 2.239 3.040 nonbonded pdb=" O ASP B 490 " pdb=" OG1 THR B 736 " model vdw 2.240 3.040 nonbonded pdb=" OE2 GLU A 25 " pdb=" OG1 THR A 281 " model vdw 2.267 3.040 ... (remaining 250896 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 10 through 1103) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 32.070 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.105 31545 Z= 0.462 Angle : 1.318 14.561 42554 Z= 0.672 Chirality : 0.062 0.350 4682 Planarity : 0.008 0.135 5306 Dihedral : 14.930 176.918 11647 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 1.00 % Allowed : 11.37 % Favored : 87.63 % Rotamer: Outliers : 1.00 % Allowed : 6.33 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 5.77 % Twisted General : 0.92 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.19 (0.10), residues: 3800 helix: -3.51 (0.07), residues: 1814 sheet: -3.49 (0.23), residues: 342 loop : -3.19 (0.13), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 715 TYR 0.034 0.003 TYR E 149 PHE 0.037 0.004 PHE C 133 TRP 0.037 0.004 TRP A 130 HIS 0.015 0.004 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.01000 (31535) covalent geometry : angle 1.31812 (42534) SS BOND : bond 0.00918 ( 10) SS BOND : angle 1.08789 ( 20) hydrogen bonds : bond 0.28342 ( 1236) hydrogen bonds : angle 9.93656 ( 3612) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 747 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7324 (pt) REVERT: A 137 TYR cc_start: 0.8544 (p90) cc_final: 0.8272 (p90) REVERT: A 440 TYR cc_start: 0.7633 (p90) cc_final: 0.7357 (p90) REVERT: A 518 LEU cc_start: 0.8968 (pp) cc_final: 0.8668 (pp) REVERT: A 814 PHE cc_start: 0.8647 (t80) cc_final: 0.8377 (t80) REVERT: A 906 VAL cc_start: 0.5459 (OUTLIER) cc_final: 0.5185 (p) REVERT: A 1022 VAL cc_start: 0.9150 (m) cc_final: 0.8732 (p) REVERT: B 478 PRO cc_start: 0.5145 (Cg_endo) cc_final: 0.4701 (Cg_exo) REVERT: B 626 VAL cc_start: 0.9569 (t) cc_final: 0.9313 (m) REVERT: B 683 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.6944 (m) REVERT: B 695 LYS cc_start: 0.8469 (mmpt) cc_final: 0.7803 (tptt) REVERT: B 704 LEU cc_start: 0.8622 (pt) cc_final: 0.8081 (pt) REVERT: B 708 MET cc_start: 0.8244 (mtt) cc_final: 0.7935 (ttm) REVERT: B 711 TYR cc_start: 0.8241 (t80) cc_final: 0.7968 (t80) REVERT: C 137 TYR cc_start: 0.8559 (p90) cc_final: 0.8265 (p90) REVERT: C 440 TYR cc_start: 0.7586 (p90) cc_final: 0.7298 (p90) REVERT: C 518 LEU cc_start: 0.9130 (pp) cc_final: 0.8866 (pp) REVERT: C 814 PHE cc_start: 0.8604 (t80) cc_final: 0.8217 (t80) REVERT: C 906 VAL cc_start: 0.5542 (OUTLIER) cc_final: 0.5283 (p) REVERT: C 1022 VAL cc_start: 0.9105 (m) cc_final: 0.8716 (p) REVERT: D 140 ASP cc_start: 0.6617 (t70) cc_final: 0.6282 (t0) REVERT: D 478 PRO cc_start: 0.4901 (Cg_endo) cc_final: 0.4408 (Cg_exo) REVERT: D 503 MET cc_start: 0.7892 (ttm) cc_final: 0.7638 (ttm) REVERT: D 533 TYR cc_start: 0.8497 (t80) cc_final: 0.8270 (t80) REVERT: D 626 VAL cc_start: 0.9464 (t) cc_final: 0.9087 (m) REVERT: D 683 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.7414 (m) REVERT: D 704 LEU cc_start: 0.8445 (pt) cc_final: 0.8217 (pt) REVERT: D 807 MET cc_start: 0.7866 (mtp) cc_final: 0.7606 (tmm) REVERT: F 21 ILE cc_start: 0.8384 (pt) cc_final: 0.8118 (mt) outliers start: 33 outliers final: 6 residues processed: 772 average time/residue: 0.2209 time to fit residues: 267.4782 Evaluate side-chains 393 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 382 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 683 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 0.0980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 274 HIS A 318 ASN A 337 GLN A 344 ASN ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN A 920 ASN B 10 ASN B 46 HIS B 54 ASN B 164 ASN B 214 HIS B 318 ASN B 335 GLN B 337 GLN B 344 ASN B 392 GLN B 411 ASN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN C 10 ASN C 83 ASN C 274 HIS C 318 ASN C 337 GLN C 344 ASN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 ASN ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 ASN C 985 ASN D 10 ASN D 46 HIS D 54 ASN D 164 ASN D 214 HIS D 318 ASN D 335 GLN D 337 GLN D 344 ASN D 355 ASN D 392 GLN D 411 ASN D 461 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.156631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.123497 restraints weight = 75423.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.121713 restraints weight = 68435.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.120941 restraints weight = 43937.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.120592 restraints weight = 37675.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.121114 restraints weight = 34896.773| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31545 Z= 0.142 Angle : 0.739 9.689 42554 Z= 0.387 Chirality : 0.044 0.171 4682 Planarity : 0.006 0.090 5306 Dihedral : 14.559 177.108 4593 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.37 % Favored : 90.32 % Rotamer: Outliers : 2.89 % Allowed : 11.38 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.73 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.40 (0.12), residues: 3800 helix: -1.44 (0.11), residues: 1882 sheet: -2.59 (0.24), residues: 350 loop : -3.14 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 108 TYR 0.028 0.002 TYR C 980 PHE 0.041 0.002 PHE A 965 TRP 0.020 0.001 TRP A 460 HIS 0.004 0.001 HIS F 27 Details of bonding type rmsd covalent geometry : bond 0.00304 (31535) covalent geometry : angle 0.73895 (42534) SS BOND : bond 0.00569 ( 10) SS BOND : angle 1.15102 ( 20) hydrogen bonds : bond 0.04010 ( 1236) hydrogen bonds : angle 5.01042 ( 3612) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 517 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 852 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8041 (pt) REVERT: A 938 PHE cc_start: 0.8497 (m-80) cc_final: 0.8259 (m-10) REVERT: A 1000 ASN cc_start: 0.6788 (m-40) cc_final: 0.6423 (m-40) REVERT: B 138 ASP cc_start: 0.7503 (t0) cc_final: 0.7017 (t0) REVERT: B 140 ASP cc_start: 0.5777 (t70) cc_final: 0.4682 (t0) REVERT: B 231 ASP cc_start: 0.7475 (t70) cc_final: 0.7159 (p0) REVERT: B 408 MET cc_start: 0.6542 (tmm) cc_final: 0.6299 (tmm) REVERT: B 449 LYS cc_start: 0.6258 (mmtm) cc_final: 0.5946 (mmmt) REVERT: B 669 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.9031 (ptpp) REVERT: B 673 TYR cc_start: 0.7406 (m-80) cc_final: 0.6989 (m-80) REVERT: B 695 LYS cc_start: 0.8342 (mmpt) cc_final: 0.7756 (tptt) REVERT: B 711 TYR cc_start: 0.7966 (t80) cc_final: 0.7532 (t80) REVERT: B 712 ILE cc_start: 0.9359 (mm) cc_final: 0.9137 (mm) REVERT: B 788 SER cc_start: 0.8276 (p) cc_final: 0.7975 (p) REVERT: C 71 TYR cc_start: 0.4512 (m-80) cc_final: 0.4105 (m-80) REVERT: C 533 TYR cc_start: 0.8027 (t80) cc_final: 0.7807 (t80) REVERT: C 814 PHE cc_start: 0.8149 (t80) cc_final: 0.7916 (t80) REVERT: C 852 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.7951 (pt) REVERT: C 1000 ASN cc_start: 0.6832 (m-40) cc_final: 0.6440 (m-40) REVERT: C 1022 VAL cc_start: 0.9063 (m) cc_final: 0.8796 (p) REVERT: D 140 ASP cc_start: 0.5695 (t70) cc_final: 0.4738 (t0) REVERT: D 231 ASP cc_start: 0.7330 (t70) cc_final: 0.7058 (p0) REVERT: D 269 GLU cc_start: 0.7245 (tp30) cc_final: 0.6907 (tp30) REVERT: D 669 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.9082 (ptpp) REVERT: D 673 TYR cc_start: 0.7312 (m-80) cc_final: 0.6771 (m-80) REVERT: D 695 LYS cc_start: 0.8357 (mmmt) cc_final: 0.7825 (tptt) REVERT: D 788 SER cc_start: 0.8623 (p) cc_final: 0.8162 (t) REVERT: E 5 PHE cc_start: 0.8863 (t80) cc_final: 0.8657 (t80) REVERT: E 101 HIS cc_start: 0.5157 (m-70) cc_final: 0.4842 (m-70) REVERT: E 123 MET cc_start: 0.4224 (mmm) cc_final: 0.3482 (mmm) REVERT: F 123 MET cc_start: 0.3991 (mmm) cc_final: 0.3531 (mmm) outliers start: 95 outliers final: 39 residues processed: 586 average time/residue: 0.2099 time to fit residues: 197.0603 Evaluate side-chains 428 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 385 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 901 PHE Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 95 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 162 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 chunk 14 optimal weight: 0.3980 chunk 318 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 131 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 182 GLN A 435 HIS B 164 ASN B 355 ASN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.155942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.116065 restraints weight = 75266.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.116868 restraints weight = 45714.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.117227 restraints weight = 35002.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.117694 restraints weight = 34660.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.117758 restraints weight = 32090.522| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31545 Z= 0.137 Angle : 0.707 16.128 42554 Z= 0.363 Chirality : 0.043 0.287 4682 Planarity : 0.005 0.079 5306 Dihedral : 13.756 178.180 4587 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.74 % Favored : 90.00 % Rotamer: Outliers : 2.74 % Allowed : 14.18 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.67 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.55 (0.13), residues: 3800 helix: -0.55 (0.11), residues: 1902 sheet: -2.59 (0.23), residues: 376 loop : -2.92 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 675 TYR 0.028 0.001 TYR C 980 PHE 0.031 0.002 PHE A 965 TRP 0.020 0.001 TRP A 460 HIS 0.021 0.002 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00303 (31535) covalent geometry : angle 0.70690 (42534) SS BOND : bond 0.00677 ( 10) SS BOND : angle 1.21753 ( 20) hydrogen bonds : bond 0.03499 ( 1236) hydrogen bonds : angle 4.48134 ( 3612) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 440 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.8262 (t80) cc_final: 0.8007 (t80) REVERT: A 585 MET cc_start: 0.8422 (mmm) cc_final: 0.8195 (mmt) REVERT: A 647 TYR cc_start: 0.8060 (p90) cc_final: 0.7822 (p90) REVERT: A 852 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8047 (pt) REVERT: A 1000 ASN cc_start: 0.6645 (m-40) cc_final: 0.6272 (m-40) REVERT: B 111 ILE cc_start: 0.7511 (mp) cc_final: 0.7290 (mm) REVERT: B 138 ASP cc_start: 0.7579 (t0) cc_final: 0.7162 (t0) REVERT: B 140 ASP cc_start: 0.6036 (t70) cc_final: 0.5321 (t0) REVERT: B 673 TYR cc_start: 0.7719 (m-80) cc_final: 0.7359 (m-80) REVERT: B 695 LYS cc_start: 0.8288 (mmpt) cc_final: 0.7777 (tptt) REVERT: B 789 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8680 (tt) REVERT: C 71 TYR cc_start: 0.4721 (m-80) cc_final: 0.3713 (m-80) REVERT: C 74 PHE cc_start: 0.8290 (t80) cc_final: 0.7988 (t80) REVERT: C 306 ILE cc_start: 0.3838 (OUTLIER) cc_final: 0.3606 (pp) REVERT: C 647 TYR cc_start: 0.8053 (p90) cc_final: 0.7816 (p90) REVERT: C 814 PHE cc_start: 0.8206 (t80) cc_final: 0.7940 (t80) REVERT: C 852 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7962 (pt) REVERT: C 886 LEU cc_start: 0.8524 (mt) cc_final: 0.8222 (pt) REVERT: C 1000 ASN cc_start: 0.6731 (m-40) cc_final: 0.6155 (m-40) REVERT: C 1022 VAL cc_start: 0.9024 (m) cc_final: 0.8704 (p) REVERT: D 113 MET cc_start: 0.8087 (mpp) cc_final: 0.7291 (mpp) REVERT: D 673 TYR cc_start: 0.7648 (m-80) cc_final: 0.7445 (m-80) REVERT: D 695 LYS cc_start: 0.8390 (mmmt) cc_final: 0.7832 (tptt) REVERT: D 713 GLU cc_start: 0.9173 (tt0) cc_final: 0.8451 (tt0) REVERT: D 788 SER cc_start: 0.8525 (p) cc_final: 0.8127 (t) REVERT: D 789 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8680 (tt) REVERT: E 5 PHE cc_start: 0.8841 (t80) cc_final: 0.8534 (t80) REVERT: E 123 MET cc_start: 0.4274 (mmm) cc_final: 0.3586 (mmm) REVERT: F 17 CYS cc_start: 0.7638 (m) cc_final: 0.7291 (m) REVERT: F 123 MET cc_start: 0.4209 (mmm) cc_final: 0.3764 (mmm) outliers start: 90 outliers final: 48 residues processed: 503 average time/residue: 0.1519 time to fit residues: 125.7136 Evaluate side-chains 412 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 359 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 901 PHE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 95 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 168 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 348 optimal weight: 0.8980 chunk 180 optimal weight: 0.3980 chunk 233 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 287 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN B 274 HIS B 587 GLN D 587 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.153754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.122788 restraints weight = 75021.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.115969 restraints weight = 71632.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.117556 restraints weight = 54452.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.118172 restraints weight = 37167.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.118083 restraints weight = 35144.830| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31545 Z= 0.170 Angle : 0.705 14.751 42554 Z= 0.361 Chirality : 0.044 0.249 4682 Planarity : 0.005 0.074 5306 Dihedral : 13.432 176.032 4585 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.55 % Favored : 89.32 % Rotamer: Outliers : 2.95 % Allowed : 16.52 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.46 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.13), residues: 3800 helix: -0.05 (0.12), residues: 1902 sheet: -2.47 (0.24), residues: 354 loop : -2.80 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 991 TYR 0.027 0.002 TYR C 980 PHE 0.023 0.002 PHE A 965 TRP 0.018 0.001 TRP A 460 HIS 0.006 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00385 (31535) covalent geometry : angle 0.70433 (42534) SS BOND : bond 0.00292 ( 10) SS BOND : angle 1.05079 ( 20) hydrogen bonds : bond 0.03294 ( 1236) hydrogen bonds : angle 4.31729 ( 3612) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 405 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.6098 (t0) cc_final: 0.5872 (t0) REVERT: A 541 PHE cc_start: 0.7893 (t80) cc_final: 0.7609 (t80) REVERT: A 647 TYR cc_start: 0.8131 (p90) cc_final: 0.7856 (p90) REVERT: A 670 MET cc_start: 0.8145 (mtp) cc_final: 0.7658 (mtm) REVERT: A 852 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7782 (pt) REVERT: A 966 PHE cc_start: 0.7783 (m-80) cc_final: 0.7572 (m-10) REVERT: B 111 ILE cc_start: 0.7611 (mp) cc_final: 0.7358 (mm) REVERT: B 138 ASP cc_start: 0.7597 (t0) cc_final: 0.7299 (t0) REVERT: B 140 ASP cc_start: 0.5941 (t70) cc_final: 0.5380 (t0) REVERT: B 408 MET cc_start: 0.6095 (tmm) cc_final: 0.5834 (tmm) REVERT: B 476 ILE cc_start: 0.4336 (OUTLIER) cc_final: 0.3902 (pt) REVERT: B 695 LYS cc_start: 0.8125 (mmpt) cc_final: 0.7799 (tptt) REVERT: B 789 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8731 (tt) REVERT: C 647 TYR cc_start: 0.8123 (p90) cc_final: 0.7860 (p90) REVERT: C 852 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7768 (pt) REVERT: C 1022 VAL cc_start: 0.9074 (m) cc_final: 0.8809 (p) REVERT: D 111 ILE cc_start: 0.7967 (mp) cc_final: 0.7621 (mm) REVERT: D 113 MET cc_start: 0.7731 (mpp) cc_final: 0.7420 (mpp) REVERT: D 408 MET cc_start: 0.5724 (tmm) cc_final: 0.5505 (tmm) REVERT: D 518 LEU cc_start: 0.9000 (pp) cc_final: 0.8689 (pp) REVERT: D 673 TYR cc_start: 0.7537 (m-80) cc_final: 0.7296 (m-80) REVERT: D 695 LYS cc_start: 0.8132 (mmmt) cc_final: 0.7764 (tptt) REVERT: D 789 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8768 (tt) REVERT: E 5 PHE cc_start: 0.8959 (t80) cc_final: 0.8736 (t80) REVERT: E 11 MET cc_start: 0.8421 (mtt) cc_final: 0.8100 (mtt) REVERT: E 123 MET cc_start: 0.4492 (mmm) cc_final: 0.3836 (mmm) REVERT: F 123 MET cc_start: 0.4014 (mmm) cc_final: 0.3498 (mmm) outliers start: 97 outliers final: 62 residues processed: 475 average time/residue: 0.1819 time to fit residues: 144.2330 Evaluate side-chains 425 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 358 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 901 PHE Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 710 GLU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 95 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 187 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 108 optimal weight: 0.0170 chunk 354 optimal weight: 4.9990 chunk 206 optimal weight: 0.0970 chunk 379 optimal weight: 20.0000 chunk 286 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.9418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 246 GLN C 147 GLN D 224 ASN D 246 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.155521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.118414 restraints weight = 75568.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.118060 restraints weight = 51298.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.118281 restraints weight = 43248.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.118875 restraints weight = 40097.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.119026 restraints weight = 36623.183| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31545 Z= 0.128 Angle : 0.674 15.112 42554 Z= 0.344 Chirality : 0.043 0.210 4682 Planarity : 0.004 0.076 5306 Dihedral : 13.115 170.660 4585 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.61 % Favored : 90.29 % Rotamer: Outliers : 3.10 % Allowed : 16.71 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.14), residues: 3800 helix: 0.26 (0.12), residues: 1906 sheet: -2.44 (0.24), residues: 352 loop : -2.68 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 991 TYR 0.029 0.001 TYR A 980 PHE 0.021 0.001 PHE A 965 TRP 0.019 0.001 TRP C 887 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00285 (31535) covalent geometry : angle 0.67344 (42534) SS BOND : bond 0.00517 ( 10) SS BOND : angle 1.10204 ( 20) hydrogen bonds : bond 0.03035 ( 1236) hydrogen bonds : angle 4.13750 ( 3612) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 409 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.6135 (t0) cc_final: 0.5888 (t0) REVERT: A 408 MET cc_start: 0.7927 (tpp) cc_final: 0.7355 (tpp) REVERT: A 585 MET cc_start: 0.8529 (mmm) cc_final: 0.8118 (mmt) REVERT: A 647 TYR cc_start: 0.8109 (p90) cc_final: 0.7810 (p90) REVERT: A 670 MET cc_start: 0.8453 (mtp) cc_final: 0.7930 (mtm) REVERT: A 852 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7931 (pt) REVERT: A 886 LEU cc_start: 0.8413 (pt) cc_final: 0.7737 (mt) REVERT: B 111 ILE cc_start: 0.7627 (mp) cc_final: 0.7382 (mm) REVERT: B 138 ASP cc_start: 0.7606 (t0) cc_final: 0.7319 (t0) REVERT: B 140 ASP cc_start: 0.6212 (t70) cc_final: 0.5843 (t0) REVERT: B 408 MET cc_start: 0.6231 (tmm) cc_final: 0.5998 (tmm) REVERT: B 479 LEU cc_start: 0.7835 (mt) cc_final: 0.7202 (mp) REVERT: B 695 LYS cc_start: 0.8196 (mmpt) cc_final: 0.7928 (tptt) REVERT: B 789 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8453 (tt) REVERT: C 71 TYR cc_start: 0.6724 (m-80) cc_final: 0.5965 (m-80) REVERT: C 306 ILE cc_start: 0.3598 (OUTLIER) cc_final: 0.3318 (pp) REVERT: C 408 MET cc_start: 0.7963 (tpp) cc_final: 0.7548 (tpp) REVERT: C 541 PHE cc_start: 0.7952 (t80) cc_final: 0.7617 (t80) REVERT: C 647 TYR cc_start: 0.8137 (p90) cc_final: 0.7913 (p90) REVERT: C 852 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7856 (pt) REVERT: C 1022 VAL cc_start: 0.9022 (m) cc_final: 0.8791 (p) REVERT: D 111 ILE cc_start: 0.8013 (mp) cc_final: 0.7683 (mm) REVERT: D 113 MET cc_start: 0.7859 (mpp) cc_final: 0.7375 (mpp) REVERT: D 449 LYS cc_start: 0.7187 (mmmt) cc_final: 0.6723 (tmtt) REVERT: D 476 ILE cc_start: 0.4537 (OUTLIER) cc_final: 0.4231 (pt) REVERT: D 503 MET cc_start: 0.8046 (tpt) cc_final: 0.7770 (tpt) REVERT: D 518 LEU cc_start: 0.9022 (pp) cc_final: 0.8725 (pp) REVERT: D 673 TYR cc_start: 0.7727 (m-80) cc_final: 0.7442 (m-80) REVERT: D 695 LYS cc_start: 0.8295 (mmmt) cc_final: 0.7946 (tptt) REVERT: D 789 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8658 (tt) REVERT: E 5 PHE cc_start: 0.8916 (t80) cc_final: 0.8652 (t80) REVERT: E 11 MET cc_start: 0.8383 (mtt) cc_final: 0.8043 (mtt) REVERT: E 123 MET cc_start: 0.4841 (mmm) cc_final: 0.4216 (mmm) REVERT: F 95 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7883 (mt) REVERT: F 123 MET cc_start: 0.4324 (mmm) cc_final: 0.3943 (mmm) outliers start: 102 outliers final: 64 residues processed: 480 average time/residue: 0.1857 time to fit residues: 148.5528 Evaluate side-chains 437 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 366 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 901 PHE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 309 ARG Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 700 TYR Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 95 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 81 optimal weight: 6.9990 chunk 369 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 361 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 231 optimal weight: 2.9990 chunk 256 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 363 optimal weight: 30.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 HIS A 147 GLN ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS C 147 GLN D 224 ASN D 298 ASN ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.148478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.116770 restraints weight = 75451.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.110322 restraints weight = 80415.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.109248 restraints weight = 58233.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.109912 restraints weight = 46795.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.110122 restraints weight = 42820.218| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 31545 Z= 0.318 Angle : 0.833 14.840 42554 Z= 0.427 Chirality : 0.049 0.206 4682 Planarity : 0.005 0.094 5306 Dihedral : 13.688 176.160 4585 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.95 % Favored : 87.79 % Rotamer: Outliers : 3.53 % Allowed : 17.38 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.13), residues: 3800 helix: 0.09 (0.12), residues: 1872 sheet: -2.57 (0.25), residues: 362 loop : -2.84 (0.14), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 309 TYR 0.029 0.002 TYR A 980 PHE 0.033 0.002 PHE A1007 TRP 0.013 0.002 TRP B 323 HIS 0.009 0.002 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00720 (31535) covalent geometry : angle 0.83257 (42534) SS BOND : bond 0.00856 ( 10) SS BOND : angle 1.38948 ( 20) hydrogen bonds : bond 0.03778 ( 1236) hydrogen bonds : angle 4.66103 ( 3612) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 361 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.4794 (m-80) cc_final: 0.4370 (m-10) REVERT: A 382 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7622 (tm) REVERT: A 518 LEU cc_start: 0.9136 (pp) cc_final: 0.8911 (pp) REVERT: A 852 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8053 (pt) REVERT: B 111 ILE cc_start: 0.7811 (mp) cc_final: 0.7547 (mm) REVERT: B 138 ASP cc_start: 0.7949 (t0) cc_final: 0.7636 (t0) REVERT: B 140 ASP cc_start: 0.6166 (t70) cc_final: 0.5729 (t0) REVERT: B 449 LYS cc_start: 0.7007 (mmmt) cc_final: 0.6512 (tmtt) REVERT: B 476 ILE cc_start: 0.4422 (OUTLIER) cc_final: 0.4037 (pt) REVERT: B 695 LYS cc_start: 0.8199 (mmpt) cc_final: 0.7902 (tptt) REVERT: B 732 TYR cc_start: 0.6923 (OUTLIER) cc_final: 0.6581 (m-80) REVERT: B 789 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9025 (tt) REVERT: C 382 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7720 (tm) REVERT: C 518 LEU cc_start: 0.9161 (pp) cc_final: 0.8952 (pp) REVERT: C 533 TYR cc_start: 0.8229 (t80) cc_final: 0.7967 (t80) REVERT: C 852 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7979 (pt) REVERT: D 111 ILE cc_start: 0.8035 (mp) cc_final: 0.7686 (mm) REVERT: D 695 LYS cc_start: 0.8269 (mmmt) cc_final: 0.8013 (tptt) REVERT: D 788 SER cc_start: 0.8697 (p) cc_final: 0.8454 (t) REVERT: D 789 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9021 (tt) REVERT: E 123 MET cc_start: 0.4721 (mmm) cc_final: 0.4208 (mmm) REVERT: E 146 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8605 (t80) REVERT: F 11 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8145 (mtt) REVERT: F 123 MET cc_start: 0.4275 (mmm) cc_final: 0.3946 (mmm) outliers start: 116 outliers final: 79 residues processed: 447 average time/residue: 0.1713 time to fit residues: 129.6558 Evaluate side-chains 408 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 319 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 706 SER Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 146 PHE Chi-restraints excluded: chain F residue 11 MET Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 153 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 141 optimal weight: 9.9990 chunk 338 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 353 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 264 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN D 224 ASN ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.151956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.122490 restraints weight = 75349.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.114401 restraints weight = 77544.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.116374 restraints weight = 66067.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.116616 restraints weight = 43149.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.116949 restraints weight = 39831.963| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31545 Z= 0.178 Angle : 0.714 14.405 42554 Z= 0.365 Chirality : 0.045 0.286 4682 Planarity : 0.005 0.091 5306 Dihedral : 13.200 174.344 4585 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.00 % Favored : 89.89 % Rotamer: Outliers : 2.86 % Allowed : 18.62 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.13), residues: 3800 helix: 0.30 (0.12), residues: 1888 sheet: -2.59 (0.25), residues: 350 loop : -2.85 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 684 TYR 0.034 0.002 TYR A 980 PHE 0.029 0.002 PHE A1007 TRP 0.021 0.001 TRP C 887 HIS 0.005 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00404 (31535) covalent geometry : angle 0.71359 (42534) SS BOND : bond 0.00211 ( 10) SS BOND : angle 1.07639 ( 20) hydrogen bonds : bond 0.03246 ( 1236) hydrogen bonds : angle 4.32114 ( 3612) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 361 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.4502 (m-80) cc_final: 0.4242 (m-80) REVERT: A 382 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7637 (tm) REVERT: A 518 LEU cc_start: 0.8961 (pp) cc_final: 0.8738 (pp) REVERT: B 138 ASP cc_start: 0.7846 (t0) cc_final: 0.7526 (t0) REVERT: B 140 ASP cc_start: 0.6157 (t70) cc_final: 0.5810 (t0) REVERT: B 476 ILE cc_start: 0.4124 (OUTLIER) cc_final: 0.3751 (pt) REVERT: B 620 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9359 (tp) REVERT: B 732 TYR cc_start: 0.6617 (OUTLIER) cc_final: 0.6125 (m-80) REVERT: B 789 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8879 (tt) REVERT: C 382 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7758 (tm) REVERT: C 456 ASP cc_start: 0.7566 (p0) cc_final: 0.7357 (p0) REVERT: C 518 LEU cc_start: 0.8923 (pp) cc_final: 0.8699 (pp) REVERT: C 852 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8054 (pt) REVERT: C 864 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6760 (mt) REVERT: C 999 PHE cc_start: 0.6080 (m-80) cc_final: 0.5764 (m-80) REVERT: D 111 ILE cc_start: 0.7914 (mp) cc_final: 0.7635 (mm) REVERT: D 138 ASP cc_start: 0.7771 (t0) cc_final: 0.6887 (t0) REVERT: D 479 LEU cc_start: 0.7804 (tt) cc_final: 0.7533 (mt) REVERT: D 673 TYR cc_start: 0.7703 (m-80) cc_final: 0.7395 (m-80) REVERT: D 695 LYS cc_start: 0.8245 (mmmt) cc_final: 0.7976 (tptp) REVERT: D 788 SER cc_start: 0.8526 (p) cc_final: 0.8235 (t) REVERT: D 789 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8826 (tt) REVERT: E 123 MET cc_start: 0.4725 (mmm) cc_final: 0.4231 (mmm) REVERT: E 146 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8550 (t80) REVERT: F 11 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8010 (mtt) REVERT: F 123 MET cc_start: 0.4086 (mmm) cc_final: 0.3764 (mmm) outliers start: 94 outliers final: 59 residues processed: 431 average time/residue: 0.1739 time to fit residues: 127.7376 Evaluate side-chains 406 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 336 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 146 PHE Chi-restraints excluded: chain F residue 11 MET Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 153 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 161 optimal weight: 5.9990 chunk 381 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 225 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 246 optimal weight: 0.3980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 412 HIS ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN B 355 ASN C 412 HIS ** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.153678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.124601 restraints weight = 75621.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.119705 restraints weight = 75197.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.120240 restraints weight = 56351.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.120574 restraints weight = 41070.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.120592 restraints weight = 38220.188| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 31545 Z= 0.138 Angle : 0.699 14.669 42554 Z= 0.354 Chirality : 0.044 0.271 4682 Planarity : 0.004 0.087 5306 Dihedral : 12.757 167.973 4585 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.34 % Favored : 89.55 % Rotamer: Outliers : 2.68 % Allowed : 19.51 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.14), residues: 3800 helix: 0.54 (0.12), residues: 1886 sheet: -2.47 (0.25), residues: 360 loop : -2.77 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 991 TYR 0.032 0.001 TYR A 980 PHE 0.021 0.001 PHE A1007 TRP 0.032 0.001 TRP A 887 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00316 (31535) covalent geometry : angle 0.69913 (42534) SS BOND : bond 0.00155 ( 10) SS BOND : angle 0.99334 ( 20) hydrogen bonds : bond 0.03054 ( 1236) hydrogen bonds : angle 4.22049 ( 3612) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 367 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7741 (tm) REVERT: A 408 MET cc_start: 0.7530 (tpp) cc_final: 0.6433 (ttt) REVERT: A 518 LEU cc_start: 0.8807 (pp) cc_final: 0.8542 (pp) REVERT: A 708 MET cc_start: 0.8470 (mtt) cc_final: 0.8186 (mtt) REVERT: B 138 ASP cc_start: 0.7683 (t0) cc_final: 0.7385 (t0) REVERT: B 140 ASP cc_start: 0.6005 (t70) cc_final: 0.5730 (t0) REVERT: B 476 ILE cc_start: 0.4161 (OUTLIER) cc_final: 0.3769 (pt) REVERT: B 503 MET cc_start: 0.7232 (tpp) cc_final: 0.6988 (tpp) REVERT: B 629 MET cc_start: 0.8071 (tpp) cc_final: 0.7291 (mtt) REVERT: B 732 TYR cc_start: 0.6129 (OUTLIER) cc_final: 0.5580 (m-80) REVERT: B 788 SER cc_start: 0.8464 (p) cc_final: 0.8195 (m) REVERT: B 789 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8783 (tt) REVERT: C 382 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7760 (tm) REVERT: C 408 MET cc_start: 0.7653 (tpp) cc_final: 0.6622 (ttt) REVERT: C 456 ASP cc_start: 0.7252 (p0) cc_final: 0.7002 (p0) REVERT: C 518 LEU cc_start: 0.8805 (pp) cc_final: 0.8558 (pp) REVERT: D 111 ILE cc_start: 0.7806 (mp) cc_final: 0.7588 (mm) REVERT: D 138 ASP cc_start: 0.7547 (t0) cc_final: 0.6721 (t0) REVERT: D 673 TYR cc_start: 0.7546 (m-80) cc_final: 0.7287 (m-80) REVERT: D 789 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8750 (tt) REVERT: E 11 MET cc_start: 0.8295 (mtt) cc_final: 0.7953 (mtt) REVERT: E 123 MET cc_start: 0.4576 (mmm) cc_final: 0.4134 (mmm) REVERT: E 153 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7227 (tmm) REVERT: F 11 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7936 (mtt) REVERT: F 95 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7509 (mt) REVERT: F 123 MET cc_start: 0.3830 (mmm) cc_final: 0.3615 (mmm) outliers start: 88 outliers final: 58 residues processed: 426 average time/residue: 0.1617 time to fit residues: 117.7018 Evaluate side-chains 403 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 336 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain F residue 11 MET Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 153 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 346 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 236 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 233 optimal weight: 0.9980 chunk 322 optimal weight: 7.9990 chunk 197 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.153630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.123495 restraints weight = 75434.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.118867 restraints weight = 81468.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.118494 restraints weight = 57639.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.118889 restraints weight = 43477.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.119328 restraints weight = 38420.690| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 31545 Z= 0.146 Angle : 0.716 14.861 42554 Z= 0.359 Chirality : 0.044 0.268 4682 Planarity : 0.004 0.088 5306 Dihedral : 12.555 162.831 4585 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.05 % Favored : 89.84 % Rotamer: Outliers : 2.40 % Allowed : 19.90 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.88 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.14), residues: 3800 helix: 0.67 (0.12), residues: 1874 sheet: -2.31 (0.25), residues: 364 loop : -2.70 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 991 TYR 0.030 0.001 TYR A 980 PHE 0.032 0.002 PHE A 541 TRP 0.024 0.001 TRP A 887 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00334 (31535) covalent geometry : angle 0.71536 (42534) SS BOND : bond 0.00162 ( 10) SS BOND : angle 0.98701 ( 20) hydrogen bonds : bond 0.03040 ( 1236) hydrogen bonds : angle 4.18814 ( 3612) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 355 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7734 (tm) REVERT: A 408 MET cc_start: 0.7582 (tpp) cc_final: 0.6645 (ttt) REVERT: A 518 LEU cc_start: 0.8938 (pp) cc_final: 0.8691 (pp) REVERT: A 585 MET cc_start: 0.8487 (mmm) cc_final: 0.8167 (ttm) REVERT: A 708 MET cc_start: 0.8605 (mtt) cc_final: 0.8353 (mtt) REVERT: A 886 LEU cc_start: 0.8491 (pt) cc_final: 0.7508 (mt) REVERT: A 1016 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.8908 (tp) REVERT: A 1023 MET cc_start: 0.8893 (pmm) cc_final: 0.8634 (pmm) REVERT: B 138 ASP cc_start: 0.7777 (t0) cc_final: 0.7455 (t0) REVERT: B 140 ASP cc_start: 0.5993 (t70) cc_final: 0.5737 (t0) REVERT: B 476 ILE cc_start: 0.4273 (OUTLIER) cc_final: 0.3912 (pt) REVERT: B 521 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8414 (mp) REVERT: B 629 MET cc_start: 0.8043 (tpp) cc_final: 0.7317 (mtt) REVERT: B 732 TYR cc_start: 0.6680 (OUTLIER) cc_final: 0.6140 (m-80) REVERT: B 788 SER cc_start: 0.8506 (p) cc_final: 0.8264 (m) REVERT: B 789 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8826 (tt) REVERT: C 382 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7790 (tm) REVERT: C 408 MET cc_start: 0.7785 (tpp) cc_final: 0.6813 (ttt) REVERT: C 456 ASP cc_start: 0.7813 (p0) cc_final: 0.7524 (p0) REVERT: C 518 LEU cc_start: 0.8913 (pp) cc_final: 0.8668 (pp) REVERT: C 849 LEU cc_start: 0.8265 (mm) cc_final: 0.7971 (mt) REVERT: D 111 ILE cc_start: 0.7942 (mp) cc_final: 0.7663 (mm) REVERT: D 138 ASP cc_start: 0.7613 (t0) cc_final: 0.6847 (t0) REVERT: D 673 TYR cc_start: 0.7842 (m-80) cc_final: 0.7513 (m-80) REVERT: D 770 LYS cc_start: 0.1268 (OUTLIER) cc_final: 0.1002 (pmmt) REVERT: D 788 SER cc_start: 0.8455 (p) cc_final: 0.8223 (m) REVERT: D 789 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8797 (tt) REVERT: E 11 MET cc_start: 0.8296 (mtt) cc_final: 0.7961 (mtt) REVERT: E 123 MET cc_start: 0.4579 (mmm) cc_final: 0.4122 (mmm) REVERT: F 11 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7946 (mtt) REVERT: F 95 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7786 (mt) REVERT: F 123 MET cc_start: 0.3971 (mmm) cc_final: 0.3739 (mmm) outliers start: 79 outliers final: 58 residues processed: 411 average time/residue: 0.1743 time to fit residues: 122.6191 Evaluate side-chains 406 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 337 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 770 LYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 11 MET Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 153 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 93 optimal weight: 7.9990 chunk 245 optimal weight: 0.7980 chunk 131 optimal weight: 0.0070 chunk 24 optimal weight: 10.0000 chunk 283 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 310 optimal weight: 4.9990 chunk 370 optimal weight: 3.9990 chunk 305 optimal weight: 5.9990 chunk 228 optimal weight: 0.9980 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.153315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.129187 restraints weight = 75005.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.127593 restraints weight = 80257.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.125385 restraints weight = 68591.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.126082 restraints weight = 61511.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.126087 restraints weight = 45722.227| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31545 Z= 0.164 Angle : 0.734 14.491 42554 Z= 0.369 Chirality : 0.044 0.269 4682 Planarity : 0.004 0.087 5306 Dihedral : 12.511 161.763 4585 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.45 % Favored : 89.45 % Rotamer: Outliers : 2.37 % Allowed : 20.15 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.88 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.14), residues: 3800 helix: 0.69 (0.12), residues: 1872 sheet: -2.29 (0.26), residues: 350 loop : -2.68 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 108 TYR 0.032 0.002 TYR A 980 PHE 0.022 0.002 PHE A 541 TRP 0.022 0.001 TRP A 887 HIS 0.012 0.001 HIS E 107 Details of bonding type rmsd covalent geometry : bond 0.00377 (31535) covalent geometry : angle 0.73374 (42534) SS BOND : bond 0.00175 ( 10) SS BOND : angle 1.00874 ( 20) hydrogen bonds : bond 0.03087 ( 1236) hydrogen bonds : angle 4.23367 ( 3612) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 351 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7764 (tm) REVERT: A 408 MET cc_start: 0.7331 (tpp) cc_final: 0.6744 (ttt) REVERT: A 518 LEU cc_start: 0.8769 (pp) cc_final: 0.8481 (pp) REVERT: A 585 MET cc_start: 0.8441 (mmm) cc_final: 0.8208 (ttm) REVERT: A 708 MET cc_start: 0.8342 (mtt) cc_final: 0.8122 (mtt) REVERT: A 886 LEU cc_start: 0.8236 (pt) cc_final: 0.7229 (mt) REVERT: B 138 ASP cc_start: 0.7773 (t0) cc_final: 0.7422 (t0) REVERT: B 140 ASP cc_start: 0.5904 (t70) cc_final: 0.5684 (t0) REVERT: B 476 ILE cc_start: 0.3946 (OUTLIER) cc_final: 0.3565 (pt) REVERT: B 521 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8473 (mp) REVERT: B 629 MET cc_start: 0.8121 (tpp) cc_final: 0.7341 (mtt) REVERT: B 732 TYR cc_start: 0.5690 (OUTLIER) cc_final: 0.5063 (m-80) REVERT: B 788 SER cc_start: 0.8480 (p) cc_final: 0.8182 (m) REVERT: B 789 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8748 (tt) REVERT: C 382 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7834 (tm) REVERT: C 408 MET cc_start: 0.7475 (tpp) cc_final: 0.6779 (ttt) REVERT: C 518 LEU cc_start: 0.8788 (pp) cc_final: 0.8543 (pp) REVERT: C 852 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7254 (pp) REVERT: D 111 ILE cc_start: 0.7562 (mp) cc_final: 0.7337 (mm) REVERT: D 138 ASP cc_start: 0.7707 (t0) cc_final: 0.6965 (t0) REVERT: D 673 TYR cc_start: 0.7386 (m-80) cc_final: 0.7156 (m-80) REVERT: D 770 LYS cc_start: 0.1078 (OUTLIER) cc_final: 0.0683 (pmmt) REVERT: D 788 SER cc_start: 0.8441 (p) cc_final: 0.8043 (m) REVERT: D 789 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8746 (tt) REVERT: E 11 MET cc_start: 0.8192 (mtt) cc_final: 0.7932 (mtt) REVERT: E 123 MET cc_start: 0.4657 (mmm) cc_final: 0.4235 (mmm) REVERT: F 11 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7901 (mtt) REVERT: F 95 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7353 (mt) outliers start: 78 outliers final: 56 residues processed: 407 average time/residue: 0.1744 time to fit residues: 121.0768 Evaluate side-chains 397 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 330 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 770 LYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 11 MET Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 153 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 373 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 242 optimal weight: 7.9990 chunk 375 optimal weight: 10.0000 chunk 196 optimal weight: 0.0870 chunk 172 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 339 optimal weight: 5.9990 chunk 263 optimal weight: 0.0370 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 HIS B 224 ASN B 298 ASN B 587 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 HIS D 224 ASN ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.155363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.131305 restraints weight = 75630.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.129963 restraints weight = 79624.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.128249 restraints weight = 61627.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.128972 restraints weight = 52747.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.128304 restraints weight = 44658.450| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.6207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 31545 Z= 0.128 Angle : 0.715 14.452 42554 Z= 0.357 Chirality : 0.044 0.263 4682 Planarity : 0.004 0.087 5306 Dihedral : 12.226 161.791 4585 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.53 % Favored : 90.39 % Rotamer: Outliers : 1.83 % Allowed : 20.72 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.14), residues: 3800 helix: 0.86 (0.12), residues: 1874 sheet: -2.34 (0.25), residues: 360 loop : -2.61 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 675 TYR 0.028 0.001 TYR A 980 PHE 0.030 0.001 PHE A 541 TRP 0.024 0.001 TRP B 130 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00292 (31535) covalent geometry : angle 0.71471 (42534) SS BOND : bond 0.00224 ( 10) SS BOND : angle 1.12376 ( 20) hydrogen bonds : bond 0.03006 ( 1236) hydrogen bonds : angle 4.12875 ( 3612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5591.12 seconds wall clock time: 97 minutes 55.76 seconds (5875.76 seconds total)