Starting phenix.real_space_refine on Sun Jul 5 23:43:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ssa_40749/07_2026/8ssa_40749.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ssa_40749/07_2026/8ssa_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_40749/07_2026/8ssa_40749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ssa_40749/07_2026/8ssa_40749.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ssa_40749/07_2026/8ssa_40749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ssa_40749/07_2026/8ssa_40749.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ssa_40749/07_2026/8ssa_40749.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ssa_40749/07_2026/8ssa_40749.cif" } 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-dev-6108/lib/python3.11/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: 6.15, per 1000 atoms: 0.20 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: 2.69 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.95 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: 6.13 Time building geometry restraints manager: 3.47 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: 18287 35.38 - 70.77: 315 70.77 - 106.15: 27 106.15 - 141.53: 6 141.53 - 176.92: 10 Dihedral angle restraints: 18645 sinusoidal: 7563 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 18642 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: 4.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 27.490 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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 : 14.398 176.918 11527 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 are 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/Z covalent geometry : bond 0.01000 / 0.46 (31535) covalent geometry : angle 1.31812 / 0.67 (42534) SS BOND : bond 0.00918 / 0.54 ( 10) SS BOND : angle 1.08789 / 0.75 ( 20) hydrogen bonds : bond 0.28342 / 18.88 ( 1236) hydrogen bonds : angle 9.93656 / 6.91 ( 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 : 1.165 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: 0.2005 time to fit residues: 244.0273 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 : 0.983 ------------------------------------------------------------------------------- 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... 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 = 0.156608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.119121 restraints weight = 75396.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.119477 restraints weight = 46480.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.119647 restraints weight = 38044.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.120178 restraints weight = 35075.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.120415 restraints weight = 32844.117| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3173 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 9.724 42554 Z= 0.387 Chirality : 0.044 0.171 4682 Planarity : 0.006 0.090 5306 Dihedral : 13.838 177.078 4473 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.42 % Favored : 90.26 % Rotamer: Outliers : 2.89 % Allowed : 11.41 % Favored : 85.70 % 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 are not related in a simple way. whole: -3.40 (0.12), residues: 3800 helix: -1.45 (0.11), residues: 1882 sheet: -2.60 (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 0.005 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (31535) covalent geometry : angle 0.73840 / 0.39 (42534) SS BOND : bond 0.00636 / 0.41 ( 10) SS BOND : angle 1.13859 / 0.62 ( 20) hydrogen bonds : bond 0.04024 / 2.60 ( 1236) hydrogen bonds : angle 5.01656 / 3.44 ( 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 615 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 520 time to evaluate : 1.411 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: 0.8572 (OUTLIER) cc_final: 0.8062 (pt) REVERT: A 938 PHE cc_start: 0.8564 (m-80) cc_final: 0.8345 (m-10) REVERT: A 1000 ASN cc_start: 0.6824 (m-40) cc_final: 0.6436 (m-40) REVERT: A 1022 VAL cc_start: 0.9013 (m) cc_final: 0.8810 (p) REVERT: B 138 ASP cc_start: 0.7491 (t0) cc_final: 0.7015 (t0) REVERT: B 140 ASP cc_start: 0.5809 (t70) cc_final: 0.4694 (t0) REVERT: B 231 ASP cc_start: 0.7450 (t70) cc_final: 0.7141 (p0) REVERT: B 408 MET cc_start: 0.6569 (tmm) cc_final: 0.6313 (tmm) REVERT: B 449 LYS cc_start: 0.6333 (mmtm) cc_final: 0.5997 (mmmt) REVERT: B 669 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.9089 (ptpp) REVERT: B 673 TYR cc_start: 0.7474 (m-80) cc_final: 0.7031 (m-80) REVERT: B 695 LYS cc_start: 0.8361 (mmpt) cc_final: 0.7782 (tptt) REVERT: B 700 TYR cc_start: 0.5890 (t80) cc_final: 0.5689 (t80) REVERT: B 711 TYR cc_start: 0.8047 (t80) cc_final: 0.7576 (t80) REVERT: B 712 ILE cc_start: 0.9402 (mm) cc_final: 0.9166 (mm) REVERT: B 788 SER cc_start: 0.8313 (p) cc_final: 0.8020 (p) REVERT: C 71 TYR cc_start: 0.4588 (m-80) cc_final: 0.4136 (m-80) REVERT: C 814 PHE cc_start: 0.8199 (t80) cc_final: 0.7942 (t80) REVERT: C 852 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7974 (pt) REVERT: C 1000 ASN cc_start: 0.6863 (m-40) cc_final: 0.6453 (m-40) REVERT: C 1022 VAL cc_start: 0.9057 (m) cc_final: 0.8786 (p) REVERT: D 140 ASP cc_start: 0.5710 (t70) cc_final: 0.4751 (t0) REVERT: D 231 ASP cc_start: 0.7275 (t70) cc_final: 0.7050 (p0) REVERT: D 269 GLU cc_start: 0.7363 (tp30) cc_final: 0.7017 (tp30) REVERT: D 669 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.9136 (ptpp) REVERT: D 673 TYR cc_start: 0.7383 (m-80) cc_final: 0.6818 (m-80) REVERT: D 695 LYS cc_start: 0.8381 (mmmt) cc_final: 0.7855 (tptt) REVERT: D 721 MET cc_start: 0.7585 (tpp) cc_final: 0.7373 (tpp) REVERT: D 788 SER cc_start: 0.8586 (p) cc_final: 0.8081 (t) REVERT: E 5 PHE cc_start: 0.8835 (t80) cc_final: 0.8621 (t80) REVERT: E 101 HIS cc_start: 0.5113 (m-70) cc_final: 0.4814 (m-70) REVERT: E 123 MET cc_start: 0.4244 (mmm) cc_final: 0.3508 (mmm) REVERT: F 123 MET cc_start: 0.3988 (mmm) cc_final: 0.3540 (mmm) outliers start: 95 outliers final: 39 residues processed: 589 average time/residue: 0.2050 time to fit residues: 194.8771 Evaluate side-chains 429 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 386 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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: 9.9990 chunk 52 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 222 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 318 optimal weight: 0.0970 chunk 109 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 147 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.156296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.125755 restraints weight = 75295.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.119496 restraints weight = 70535.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.120850 restraints weight = 54112.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.121215 restraints weight = 37138.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.121480 restraints weight = 34302.650| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3951 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= 0.134 Angle : 0.703 16.213 42554 Z= 0.361 Chirality : 0.043 0.265 4682 Planarity : 0.005 0.079 5306 Dihedral : 13.133 178.171 4467 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.58 % Favored : 90.16 % Rotamer: Outliers : 2.74 % Allowed : 14.06 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.62 % 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 are not related in a simple way. whole: -2.53 (0.13), residues: 3800 helix: -0.55 (0.11), residues: 1900 sheet: -2.42 (0.23), residues: 374 loop : -2.94 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 675 TYR 0.026 0.001 TYR A 980 PHE 0.031 0.001 PHE A 965 TRP 0.020 0.001 TRP A 460 HIS 0.021 0.002 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (31535) covalent geometry : angle 0.70219 / 0.36 (42534) SS BOND : bond 0.01112 / 0.56 ( 10) SS BOND : angle 1.27588 / 0.59 ( 20) hydrogen bonds : bond 0.03490 / 2.25 ( 1236) hydrogen bonds : angle 4.47164 / 3.08 ( 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 537 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 447 time to evaluate : 1.467 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: A 852 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7887 (pt) REVERT: A 938 PHE cc_start: 0.8187 (m-80) cc_final: 0.7934 (m-10) REVERT: A 1000 ASN cc_start: 0.6432 (m-40) cc_final: 0.6091 (m-40) REVERT: B 138 ASP cc_start: 0.7520 (t0) cc_final: 0.7128 (t0) REVERT: B 140 ASP cc_start: 0.5943 (t70) cc_final: 0.5249 (t0) REVERT: B 673 TYR cc_start: 0.7439 (m-80) cc_final: 0.7192 (m-80) REVERT: B 695 LYS cc_start: 0.8045 (mmpt) cc_final: 0.7606 (tptt) REVERT: B 789 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8673 (tt) REVERT: C 74 PHE cc_start: 0.7925 (t80) cc_final: 0.7722 (t80) REVERT: C 852 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7831 (pt) REVERT: C 1000 ASN cc_start: 0.6564 (m-40) cc_final: 0.6227 (m-40) REVERT: D 113 MET cc_start: 0.7816 (mpp) cc_final: 0.7501 (mpp) REVERT: D 695 LYS cc_start: 0.8219 (mmmt) cc_final: 0.7702 (tptt) REVERT: D 713 GLU cc_start: 0.8967 (tt0) cc_final: 0.8471 (tt0) REVERT: D 788 SER cc_start: 0.8447 (p) cc_final: 0.8052 (t) REVERT: D 789 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8692 (tt) REVERT: E 5 PHE cc_start: 0.8936 (t80) cc_final: 0.8696 (t80) REVERT: E 60 ILE cc_start: 0.7151 (mm) cc_final: 0.6907 (tp) REVERT: E 123 MET cc_start: 0.4162 (mmm) cc_final: 0.3467 (mmm) REVERT: F 123 MET cc_start: 0.4171 (mmm) cc_final: 0.3714 (mmm) outliers start: 90 outliers final: 48 residues processed: 510 average time/residue: 0.1960 time to fit residues: 164.0370 Evaluate side-chains 409 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 357 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 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 999 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 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: 10.0000 chunk 2 optimal weight: 9.9990 chunk 348 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 233 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 287 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 GLN B 274 HIS 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.153690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.122729 restraints weight = 75318.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 91)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.114178 restraints weight = 75107.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.116490 restraints weight = 55970.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.116980 restraints weight = 36727.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.117113 restraints weight = 34522.874| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31545 Z= 0.171 Angle : 0.708 14.857 42554 Z= 0.364 Chirality : 0.044 0.250 4682 Planarity : 0.005 0.076 5306 Dihedral : 12.815 177.051 4465 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.45 % Favored : 89.42 % Rotamer: Outliers : 2.98 % Allowed : 16.40 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.48 % 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 are not related in a simple way. whole: -2.05 (0.13), residues: 3800 helix: -0.04 (0.12), residues: 1896 sheet: -2.49 (0.24), residues: 350 loop : -2.77 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 331 TYR 0.027 0.002 TYR C 980 PHE 0.023 0.002 PHE A 965 TRP 0.022 0.002 TRP A 460 HIS 0.007 0.001 HIS D 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (31535) covalent geometry : angle 0.70768 / 0.36 (42534) SS BOND : bond 0.00714 / 0.36 ( 10) SS BOND : angle 1.15827 / 0.57 ( 20) hydrogen bonds : bond 0.03287 / 2.14 ( 1236) hydrogen bonds : angle 4.29951 / 2.97 ( 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 518 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 420 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: 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: 0.6090 (t0) cc_final: 0.5876 (t0) REVERT: A 541 PHE cc_start: 0.7852 (t80) cc_final: 0.7587 (t80) REVERT: A 585 MET cc_start: 0.8390 (mmt) cc_final: 0.7576 (mmt) REVERT: A 647 TYR cc_start: 0.8073 (p90) cc_final: 0.7688 (p90) REVERT: A 852 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7815 (pt) REVERT: A 966 PHE cc_start: 0.7887 (m-80) cc_final: 0.7650 (m-10) REVERT: B 138 ASP cc_start: 0.7594 (t0) cc_final: 0.7297 (t0) REVERT: B 140 ASP cc_start: 0.6009 (t70) cc_final: 0.5536 (t0) REVERT: B 408 MET cc_start: 0.6101 (tmm) cc_final: 0.5848 (tmm) REVERT: B 695 LYS cc_start: 0.8152 (mmpt) cc_final: 0.7831 (tptt) REVERT: B 789 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8736 (tt) REVERT: C 382 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7321 (tm) REVERT: C 541 PHE cc_start: 0.7911 (t80) cc_final: 0.7604 (t80) REVERT: C 647 TYR cc_start: 0.8142 (p90) cc_final: 0.7560 (p90) REVERT: C 852 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7766 (pt) REVERT: C 966 PHE cc_start: 0.7922 (m-80) cc_final: 0.7680 (m-10) REVERT: C 1022 VAL cc_start: 0.9075 (m) cc_final: 0.8856 (p) REVERT: D 111 ILE cc_start: 0.8061 (mp) cc_final: 0.7730 (mm) REVERT: D 113 MET cc_start: 0.7738 (mpp) cc_final: 0.7384 (mpp) REVERT: D 408 MET cc_start: 0.5723 (tmm) cc_final: 0.5513 (tmm) REVERT: D 518 LEU cc_start: 0.8969 (pp) cc_final: 0.8672 (pp) REVERT: D 607 PHE cc_start: 0.8887 (t80) cc_final: 0.8632 (t80) REVERT: D 673 TYR cc_start: 0.7209 (m-80) cc_final: 0.6824 (m-80) REVERT: D 695 LYS cc_start: 0.8177 (mmmt) cc_final: 0.7781 (tptt) REVERT: D 788 SER cc_start: 0.8590 (p) cc_final: 0.8254 (t) REVERT: D 789 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8710 (tt) REVERT: E 5 PHE cc_start: 0.8948 (t80) cc_final: 0.8719 (t80) REVERT: E 11 MET cc_start: 0.8424 (mtt) cc_final: 0.8091 (mtt) REVERT: E 60 ILE cc_start: 0.7097 (mm) cc_final: 0.6874 (tp) REVERT: E 123 MET cc_start: 0.4569 (mmm) cc_final: 0.3915 (mmm) REVERT: F 123 MET cc_start: 0.3987 (mmm) cc_final: 0.3504 (mmm) outliers start: 98 outliers final: 56 residues processed: 489 average time/residue: 0.1890 time to fit residues: 152.8212 Evaluate side-chains 433 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 372 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 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 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 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 700 TYR 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 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 600 ILE Chi-restraints excluded: chain C residue 649 THR 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 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 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: 0.9990 chunk 126 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 354 optimal weight: 4.9990 chunk 206 optimal weight: 0.9980 chunk 379 optimal weight: 20.0000 chunk 286 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 188 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN B 246 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.154577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.124424 restraints weight = 75659.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.115537 restraints weight = 75414.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.117118 restraints weight = 58633.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.117516 restraints weight = 38622.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.117698 restraints weight = 36503.808| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4724 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= 0.144 Angle : 0.688 15.089 42554 Z= 0.352 Chirality : 0.043 0.192 4682 Planarity : 0.005 0.079 5306 Dihedral : 12.551 177.559 4465 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.87 % Favored : 90.03 % Rotamer: Outliers : 3.13 % Allowed : 16.80 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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 are not related in a simple way. whole: -1.76 (0.13), residues: 3800 helix: 0.24 (0.12), residues: 1906 sheet: -2.45 (0.25), residues: 342 loop : -2.70 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 991 TYR 0.028 0.001 TYR A 980 PHE 0.022 0.001 PHE A 965 TRP 0.022 0.001 TRP C 887 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (31535) covalent geometry : angle 0.68808 / 0.35 (42534) SS BOND : bond 0.00552 / 0.28 ( 10) SS BOND : angle 1.10468 / 0.54 ( 20) hydrogen bonds : bond 0.03086 / 2.02 ( 1236) hydrogen bonds : angle 4.16104 / 2.89 ( 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 498 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 395 time to evaluate : 1.523 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: A 231 ASP cc_start: 0.6055 (t0) cc_final: 0.5822 (t0) REVERT: A 408 MET cc_start: 0.7902 (tpp) cc_final: 0.7436 (tpp) REVERT: A 585 MET cc_start: 0.8505 (mmt) cc_final: 0.7450 (mmt) REVERT: A 647 TYR cc_start: 0.8123 (p90) cc_final: 0.7707 (p90) REVERT: A 670 MET cc_start: 0.8323 (mtp) cc_final: 0.7791 (mtm) REVERT: A 852 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7936 (pt) REVERT: A 886 LEU cc_start: 0.8408 (pt) cc_final: 0.7688 (mt) REVERT: B 138 ASP cc_start: 0.7645 (t0) cc_final: 0.7377 (t0) REVERT: B 140 ASP cc_start: 0.6090 (t70) cc_final: 0.5737 (t0) REVERT: B 408 MET cc_start: 0.6202 (tmm) cc_final: 0.5961 (tmm) REVERT: B 476 ILE cc_start: 0.4182 (OUTLIER) cc_final: 0.3758 (pt) REVERT: B 479 LEU cc_start: 0.7782 (mt) cc_final: 0.7147 (mp) REVERT: B 684 ARG cc_start: 0.7253 (ptt-90) cc_final: 0.7026 (ptt-90) REVERT: B 695 LYS cc_start: 0.8118 (mmpt) cc_final: 0.7823 (tptt) REVERT: B 789 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8682 (tt) REVERT: C 306 ILE cc_start: 0.3579 (OUTLIER) cc_final: 0.2974 (mt) REVERT: C 408 MET cc_start: 0.7955 (tpp) cc_final: 0.7508 (tpp) REVERT: C 647 TYR cc_start: 0.8189 (p90) cc_final: 0.7565 (p90) REVERT: C 670 MET cc_start: 0.8005 (mtp) cc_final: 0.7320 (mtm) REVERT: C 852 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7790 (pt) REVERT: C 1022 VAL cc_start: 0.9091 (m) cc_final: 0.8827 (p) REVERT: D 111 ILE cc_start: 0.7972 (mp) cc_final: 0.7665 (mm) REVERT: D 113 MET cc_start: 0.7837 (mpp) cc_final: 0.7422 (mpp) REVERT: D 476 ILE cc_start: 0.4507 (OUTLIER) cc_final: 0.4173 (pt) REVERT: D 518 LEU cc_start: 0.8982 (pp) cc_final: 0.8678 (pp) REVERT: D 673 TYR cc_start: 0.7334 (m-80) cc_final: 0.7005 (m-80) REVERT: D 695 LYS cc_start: 0.8148 (mmmt) cc_final: 0.7866 (tptt) REVERT: D 789 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8724 (tt) REVERT: E 11 MET cc_start: 0.8339 (mtt) cc_final: 0.8013 (mtt) REVERT: E 60 ILE cc_start: 0.7059 (mm) cc_final: 0.6839 (tp) REVERT: E 123 MET cc_start: 0.4721 (mmm) cc_final: 0.4137 (mmm) REVERT: F 95 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7810 (mt) REVERT: F 123 MET cc_start: 0.4216 (mmm) cc_final: 0.3873 (mmm) outliers start: 103 outliers final: 66 residues processed: 467 average time/residue: 0.1832 time to fit residues: 142.6939 Evaluate side-chains 435 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 361 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 466 GLU Chi-restraints excluded: chain A residue 600 ILE 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 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 539 VAL 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 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 306 ILE Chi-restraints excluded: chain D residue 388 SER 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 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 95 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 146 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 81 optimal weight: 9.9990 chunk 369 optimal weight: 2.9990 chunk 254 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 361 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 231 optimal weight: 0.0980 chunk 256 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 363 optimal weight: 30.0000 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 HIS A 147 GLN B 298 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS C 147 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.148364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.118426 restraints weight = 75488.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.112463 restraints weight = 83377.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.111662 restraints weight = 69797.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.112328 restraints weight = 54685.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.112759 restraints weight = 45972.771| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 31545 Z= 0.310 Angle : 0.827 14.847 42554 Z= 0.425 Chirality : 0.048 0.204 4682 Planarity : 0.005 0.094 5306 Dihedral : 12.982 174.294 4465 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.26 % Allowed : 12.18 % Favored : 87.55 % Rotamer: Outliers : 3.71 % Allowed : 17.16 % Favored : 79.12 % 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 are not related in a simple way. whole: -2.05 (0.13), residues: 3800 helix: 0.05 (0.12), residues: 1870 sheet: -2.65 (0.24), residues: 370 loop : -2.82 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 309 TYR 0.030 0.002 TYR A 980 PHE 0.028 0.002 PHE E 146 TRP 0.018 0.002 TRP A 460 HIS 0.007 0.002 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00694 / 0.31 (31535) covalent geometry : angle 0.82690 / 0.43 (42534) SS BOND : bond 0.00372 / 0.22 ( 10) SS BOND : angle 1.25978 / 0.67 ( 20) hydrogen bonds : bond 0.03780 / 2.51 ( 1236) hydrogen bonds : angle 4.68660 / 3.24 ( 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 478 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 356 time to evaluate : 1.166 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: 0.4749 (m-80) cc_final: 0.4362 (m-80) REVERT: A 382 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7621 (tm) REVERT: A 518 LEU cc_start: 0.9153 (pp) cc_final: 0.8928 (pp) REVERT: A 585 MET cc_start: 0.8873 (mmt) cc_final: 0.8158 (mmm) REVERT: A 938 PHE cc_start: 0.8343 (m-80) cc_final: 0.8106 (t80) REVERT: B 138 ASP cc_start: 0.7935 (t0) cc_final: 0.7675 (t0) REVERT: B 140 ASP cc_start: 0.6180 (t70) cc_final: 0.5715 (t70) REVERT: B 408 MET cc_start: 0.6243 (tmm) cc_final: 0.6012 (tmm) REVERT: B 449 LYS cc_start: 0.7152 (mmmt) cc_final: 0.6613 (tmtt) REVERT: B 476 ILE cc_start: 0.4387 (OUTLIER) cc_final: 0.4033 (pt) REVERT: B 695 LYS cc_start: 0.8218 (mmpt) cc_final: 0.7878 (tptt) REVERT: B 732 TYR cc_start: 0.6805 (OUTLIER) cc_final: 0.6384 (m-80) REVERT: B 789 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9035 (tt) REVERT: C 71 TYR cc_start: 0.5090 (m-80) cc_final: 0.4370 (m-10) REVERT: C 382 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7580 (tm) REVERT: D 111 ILE cc_start: 0.7945 (mp) cc_final: 0.7608 (mm) REVERT: D 673 TYR cc_start: 0.7625 (m-80) cc_final: 0.7261 (m-80) REVERT: D 695 LYS cc_start: 0.8263 (mmmt) cc_final: 0.7993 (tptt) REVERT: D 789 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9024 (tt) REVERT: E 123 MET cc_start: 0.4776 (mmm) cc_final: 0.4256 (mmm) REVERT: F 11 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8150 (mtt) REVERT: F 123 MET cc_start: 0.4331 (mmm) cc_final: 0.4056 (mmm) outliers start: 122 outliers final: 80 residues processed: 448 average time/residue: 0.1659 time to fit residues: 127.3624 Evaluate side-chains 412 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 325 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 MET Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL 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 466 GLU 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 762 LEU Chi-restraints excluded: chain A residue 789 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 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 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 98 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 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 479 LEU 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 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 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 165 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 450 TYR 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 700 TYR 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 95 ILE Chi-restraints excluded: chain E residue 115 VAL 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: 6.9990 chunk 338 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 353 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 264 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 162 optimal weight: 0.8980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN B 355 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.150610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.119946 restraints weight = 75414.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.111854 restraints weight = 80917.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.112760 restraints weight = 64105.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.112936 restraints weight = 43818.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.113186 restraints weight = 42059.547| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 31545 Z= 0.199 Angle : 0.740 14.562 42554 Z= 0.378 Chirality : 0.046 0.287 4682 Planarity : 0.005 0.092 5306 Dihedral : 12.666 174.660 4465 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.29 % Favored : 89.50 % Rotamer: Outliers : 3.01 % Allowed : 18.53 % Favored : 78.45 % 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 are not related in a simple way. whole: -1.90 (0.13), residues: 3800 helix: 0.21 (0.12), residues: 1898 sheet: -2.61 (0.24), residues: 358 loop : -2.85 (0.14), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 684 TYR 0.034 0.002 TYR A 980 PHE 0.026 0.002 PHE E 146 TRP 0.023 0.002 TRP C 887 HIS 0.004 0.001 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (31535) covalent geometry : angle 0.74019 / 0.38 (42534) SS BOND : bond 0.00243 / 0.13 ( 10) SS BOND : angle 1.12955 / 0.57 ( 20) hydrogen bonds : bond 0.03268 / 2.16 ( 1236) hydrogen bonds : angle 4.43326 / 3.05 ( 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 462 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 363 time to evaluate : 1.212 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: 0.4669 (m-80) cc_final: 0.4300 (m-80) REVERT: A 382 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7610 (tm) REVERT: A 518 LEU cc_start: 0.8969 (pp) cc_final: 0.8747 (pp) REVERT: A 585 MET cc_start: 0.8771 (mmt) cc_final: 0.8072 (mmm) REVERT: B 138 ASP cc_start: 0.7877 (t0) cc_final: 0.7574 (t0) REVERT: B 140 ASP cc_start: 0.5972 (t70) cc_final: 0.5647 (t0) REVERT: B 408 MET cc_start: 0.5998 (tmm) cc_final: 0.5688 (tmm) REVERT: B 476 ILE cc_start: 0.4275 (OUTLIER) cc_final: 0.3934 (pt) REVERT: B 695 LYS cc_start: 0.8126 (mmpt) cc_final: 0.7830 (tptt) REVERT: B 732 TYR cc_start: 0.6702 (OUTLIER) cc_final: 0.6165 (m-80) REVERT: B 789 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8860 (tt) REVERT: C 71 TYR cc_start: 0.4816 (m-80) cc_final: 0.4400 (m-10) REVERT: C 382 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7564 (tm) REVERT: D 111 ILE cc_start: 0.7927 (mp) cc_final: 0.7652 (mm) REVERT: D 138 ASP cc_start: 0.7688 (t0) cc_final: 0.7026 (t0) REVERT: D 479 LEU cc_start: 0.7819 (tt) cc_final: 0.7567 (mt) REVERT: D 629 MET cc_start: 0.7568 (mtt) cc_final: 0.7351 (mtt) REVERT: D 673 TYR cc_start: 0.7649 (m-80) cc_final: 0.7356 (m-80) REVERT: D 695 LYS cc_start: 0.8206 (mmmt) cc_final: 0.7953 (tptt) REVERT: D 789 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8827 (tt) REVERT: E 123 MET cc_start: 0.4767 (mmm) cc_final: 0.4237 (mmm) REVERT: F 11 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8004 (mtt) REVERT: F 123 MET cc_start: 0.4327 (mmm) cc_final: 0.4039 (mmm) outliers start: 99 outliers final: 70 residues processed: 433 average time/residue: 0.1757 time to fit residues: 130.5643 Evaluate side-chains 397 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 320 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 401 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 600 ILE 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 1007 PHE 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 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 539 VAL 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 666 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 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 450 TYR 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 674 MET 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 67 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 VAL 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: 0.4980 chunk 381 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 225 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 246 optimal weight: 8.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 HIS B 214 HIS B 298 ASN C 412 HIS D 214 HIS ** 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** ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.153545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.124390 restraints weight = 76142.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.117653 restraints weight = 76501.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.117835 restraints weight = 60184.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.118643 restraints weight = 42492.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.118834 restraints weight = 38485.665| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 31545 Z= 0.137 Angle : 0.700 14.617 42554 Z= 0.354 Chirality : 0.044 0.277 4682 Planarity : 0.004 0.088 5306 Dihedral : 12.235 173.556 4465 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.97 % Favored : 89.89 % Rotamer: Outliers : 2.47 % Allowed : 19.93 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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 are not related in a simple way. whole: -1.57 (0.14), residues: 3800 helix: 0.53 (0.12), residues: 1904 sheet: -2.43 (0.25), residues: 368 loop : -2.77 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 991 TYR 0.033 0.001 TYR C 980 PHE 0.027 0.001 PHE C 999 TRP 0.029 0.001 TRP A 460 HIS 0.005 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (31535) covalent geometry : angle 0.69984 / 0.35 (42534) SS BOND : bond 0.00166 / 0.09 ( 10) SS BOND : angle 1.01589 / 0.49 ( 20) hydrogen bonds : bond 0.03064 / 2.03 ( 1236) hydrogen bonds : angle 4.19474 / 2.90 ( 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 458 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 377 time to evaluate : 1.291 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 382 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7618 (tm) REVERT: A 408 MET cc_start: 0.7584 (tpp) cc_final: 0.6433 (ttt) REVERT: A 518 LEU cc_start: 0.8758 (pp) cc_final: 0.8514 (pp) REVERT: A 585 MET cc_start: 0.8687 (mmt) cc_final: 0.7928 (mmt) REVERT: A 629 MET cc_start: 0.7694 (mtt) cc_final: 0.7474 (mtt) REVERT: B 76 PHE cc_start: 0.5643 (m-10) cc_final: 0.5412 (m-80) REVERT: B 138 ASP cc_start: 0.7767 (t0) cc_final: 0.7411 (t0) REVERT: B 140 ASP cc_start: 0.6109 (t70) cc_final: 0.5802 (t0) REVERT: B 408 MET cc_start: 0.6010 (tmm) cc_final: 0.5781 (tmm) REVERT: B 476 ILE cc_start: 0.4242 (OUTLIER) cc_final: 0.3871 (pt) REVERT: B 695 LYS cc_start: 0.8093 (mmpt) cc_final: 0.7870 (tptt) REVERT: B 732 TYR cc_start: 0.6434 (OUTLIER) cc_final: 0.5897 (m-80) REVERT: B 788 SER cc_start: 0.8433 (p) cc_final: 0.8160 (m) REVERT: B 789 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8716 (tt) REVERT: C 382 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7587 (tm) REVERT: C 408 MET cc_start: 0.7783 (tpp) cc_final: 0.6820 (ttt) REVERT: D 111 ILE cc_start: 0.7852 (mp) cc_final: 0.7619 (mm) REVERT: D 138 ASP cc_start: 0.7450 (t0) cc_final: 0.6808 (t0) REVERT: D 479 LEU cc_start: 0.7807 (tt) cc_final: 0.7581 (mt) REVERT: D 673 TYR cc_start: 0.7606 (m-80) cc_final: 0.7368 (m-80) REVERT: D 695 LYS cc_start: 0.8110 (mmmt) cc_final: 0.7830 (tptt) REVERT: E 123 MET cc_start: 0.4613 (mmm) cc_final: 0.4140 (mmm) REVERT: E 153 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7168 (tmm) REVERT: F 11 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.7963 (mtt) REVERT: F 95 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7644 (mt) REVERT: F 123 MET cc_start: 0.3862 (mmm) cc_final: 0.3619 (mmm) outliers start: 81 outliers final: 58 residues processed: 430 average time/residue: 0.1796 time to fit residues: 131.2012 Evaluate side-chains 411 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 345 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 466 GLU 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 789 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 1007 PHE 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 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 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 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 619 ASN Chi-restraints excluded: chain C residue 666 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 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 693 VAL Chi-restraints excluded: chain D residue 700 TYR 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 153 MET Chi-restraints excluded: chain F residue 11 MET Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 115 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 346 optimal weight: 7.9990 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: 2.9990 chunk 233 optimal weight: 3.9990 chunk 322 optimal weight: 5.9990 chunk 197 optimal weight: 0.7980 chunk 269 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 ASN B 587 GLN B 756 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.151899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.125593 restraints weight = 75396.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.122866 restraints weight = 83822.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.121099 restraints weight = 69344.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.122289 restraints weight = 58354.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.121971 restraints weight = 47489.462| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31545 Z= 0.181 Angle : 0.735 14.971 42554 Z= 0.370 Chirality : 0.045 0.274 4682 Planarity : 0.004 0.091 5306 Dihedral : 12.195 176.541 4465 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.63 % Favored : 89.26 % Rotamer: Outliers : 2.77 % Allowed : 19.87 % Favored : 77.36 % 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 are not related in a simple way. whole: -1.52 (0.14), residues: 3800 helix: 0.57 (0.12), residues: 1884 sheet: -2.42 (0.25), residues: 366 loop : -2.71 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 991 TYR 0.032 0.002 TYR C 980 PHE 0.037 0.002 PHE A 541 TRP 0.021 0.001 TRP A 460 HIS 0.004 0.001 HIS E 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (31535) covalent geometry : angle 0.73484 / 0.37 (42534) SS BOND : bond 0.00198 / 0.11 ( 10) SS BOND : angle 1.03967 / 0.51 ( 20) hydrogen bonds : bond 0.03176 / 2.11 ( 1236) hydrogen bonds : angle 4.32591 / 2.98 ( 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 442 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 351 time to evaluate : 1.269 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: 0.8047 (OUTLIER) cc_final: 0.7704 (tm) REVERT: A 408 MET cc_start: 0.7371 (tpp) cc_final: 0.6572 (ttt) REVERT: A 518 LEU cc_start: 0.8851 (pp) cc_final: 0.8589 (pp) REVERT: A 585 MET cc_start: 0.8688 (mmt) cc_final: 0.8047 (mmm) REVERT: A 629 MET cc_start: 0.7727 (mtt) cc_final: 0.7483 (mtt) REVERT: B 138 ASP cc_start: 0.7823 (t0) cc_final: 0.7488 (t0) REVERT: B 140 ASP cc_start: 0.6039 (t70) cc_final: 0.5778 (t0) REVERT: B 476 ILE cc_start: 0.4069 (OUTLIER) cc_final: 0.3704 (pt) REVERT: B 732 TYR cc_start: 0.5754 (OUTLIER) cc_final: 0.5317 (m-80) REVERT: B 788 SER cc_start: 0.8489 (p) cc_final: 0.8142 (m) REVERT: B 789 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8748 (tt) REVERT: C 382 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7600 (tm) REVERT: C 408 MET cc_start: 0.7620 (tpp) cc_final: 0.6840 (ttt) REVERT: D 111 ILE cc_start: 0.7663 (mp) cc_final: 0.7422 (mm) REVERT: D 138 ASP cc_start: 0.7667 (t0) cc_final: 0.6965 (t0) REVERT: D 770 LYS cc_start: 0.1132 (OUTLIER) cc_final: 0.0667 (pmmt) REVERT: D 789 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8876 (tt) REVERT: E 11 MET cc_start: 0.8268 (mtt) cc_final: 0.7953 (mtt) REVERT: E 123 MET cc_start: 0.4784 (mmm) cc_final: 0.4313 (mmm) REVERT: F 11 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7983 (mtt) REVERT: F 95 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7407 (mt) REVERT: F 123 MET cc_start: 0.4077 (mmm) cc_final: 0.3830 (mmm) outliers start: 91 outliers final: 70 residues processed: 412 average time/residue: 0.1768 time to fit residues: 125.1208 Evaluate side-chains 414 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 335 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 401 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 530 VAL 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 789 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 1007 PHE 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 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 360 ILE Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 524 GLU 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 708 MET 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 498 LEU Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 682 PHE 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 278 ILE Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 360 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 700 TYR Chi-restraints excluded: chain D residue 706 SER Chi-restraints excluded: chain D residue 770 LYS Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 80 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 69 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 93 optimal weight: 1.9990 chunk 245 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 283 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 310 optimal weight: 0.9980 chunk 370 optimal weight: 4.9990 chunk 305 optimal weight: 7.9990 chunk 228 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 ASN D 13 GLN D 224 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.151977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.122440 restraints weight = 75142.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.116221 restraints weight = 79819.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.117210 restraints weight = 64136.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.117949 restraints weight = 45830.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.118420 restraints weight = 41398.462| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31545 Z= 0.172 Angle : 0.737 14.863 42554 Z= 0.372 Chirality : 0.045 0.274 4682 Planarity : 0.004 0.090 5306 Dihedral : 12.109 178.631 4465 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.58 % Favored : 89.32 % Rotamer: Outliers : 2.56 % Allowed : 20.45 % Favored : 76.99 % 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 are not related in a simple way. whole: -1.47 (0.14), residues: 3800 helix: 0.64 (0.12), residues: 1884 sheet: -2.46 (0.24), residues: 376 loop : -2.69 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 108 TYR 0.032 0.002 TYR A 980 PHE 0.025 0.002 PHE E 146 TRP 0.021 0.001 TRP A 887 HIS 0.004 0.001 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (31535) covalent geometry : angle 0.73705 / 0.37 (42534) SS BOND : bond 0.00287 / 0.15 ( 10) SS BOND : angle 1.25651 / 0.60 ( 20) hydrogen bonds : bond 0.03165 / 2.12 ( 1236) hydrogen bonds : angle 4.34031 / 2.99 ( 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 432 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 348 time to evaluate : 1.152 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: 0.8148 (OUTLIER) cc_final: 0.7779 (tm) REVERT: A 408 MET cc_start: 0.7538 (tpp) cc_final: 0.6807 (ttt) REVERT: A 518 LEU cc_start: 0.8896 (pp) cc_final: 0.8629 (pp) REVERT: A 585 MET cc_start: 0.8842 (mmt) cc_final: 0.8137 (mmm) REVERT: A 629 MET cc_start: 0.7746 (mtt) cc_final: 0.7537 (mtt) REVERT: B 138 ASP cc_start: 0.7861 (t0) cc_final: 0.7541 (t0) REVERT: B 140 ASP cc_start: 0.6117 (t70) cc_final: 0.5858 (t0) REVERT: B 270 TYR cc_start: 0.6161 (m-80) cc_final: 0.5921 (m-80) REVERT: B 476 ILE cc_start: 0.4030 (OUTLIER) cc_final: 0.3675 (pt) REVERT: B 732 TYR cc_start: 0.6295 (OUTLIER) cc_final: 0.5812 (m-80) REVERT: B 788 SER cc_start: 0.8504 (p) cc_final: 0.8230 (m) REVERT: B 789 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8825 (tt) REVERT: C 408 MET cc_start: 0.7854 (tpp) cc_final: 0.6958 (ttt) REVERT: D 111 ILE cc_start: 0.7926 (mp) cc_final: 0.7679 (mm) REVERT: D 138 ASP cc_start: 0.7734 (t0) cc_final: 0.7065 (t0) REVERT: D 270 TYR cc_start: 0.6218 (m-80) cc_final: 0.5901 (m-80) REVERT: D 479 LEU cc_start: 0.7743 (mt) cc_final: 0.7231 (mp) REVERT: D 770 LYS cc_start: 0.1060 (OUTLIER) cc_final: 0.0514 (pmmt) REVERT: D 789 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8954 (tt) REVERT: E 11 MET cc_start: 0.8308 (mtt) cc_final: 0.7955 (mtt) REVERT: E 81 MET cc_start: 0.8522 (ttp) cc_final: 0.8134 (ttp) REVERT: E 123 MET cc_start: 0.4621 (mmm) cc_final: 0.4123 (mmm) REVERT: F 11 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.7979 (mtt) REVERT: F 95 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7646 (mt) REVERT: F 123 MET cc_start: 0.4320 (mmm) cc_final: 0.4106 (mmm) outliers start: 84 outliers final: 70 residues processed: 406 average time/residue: 0.1771 time to fit residues: 123.2155 Evaluate side-chains 409 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 331 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 401 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 530 VAL 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 789 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 1007 PHE Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1025 VAL 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 360 ILE Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 524 GLU 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 708 MET 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 415 LEU Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 498 LEU 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 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 242 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 360 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 700 TYR Chi-restraints excluded: chain D residue 706 SER Chi-restraints excluded: chain D residue 770 LYS Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 80 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 69 VAL 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: 4.9990 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 242 optimal weight: 5.9990 chunk 375 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 339 optimal weight: 4.9990 chunk 263 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.153978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.129966 restraints weight = 75688.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.125817 restraints weight = 86655.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.123741 restraints weight = 80598.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.124449 restraints weight = 61826.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.124825 restraints weight = 49861.533| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.6259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 31545 Z= 0.140 Angle : 0.726 15.449 42554 Z= 0.363 Chirality : 0.044 0.267 4682 Planarity : 0.004 0.090 5306 Dihedral : 11.891 178.951 4465 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.11 % Favored : 89.79 % Rotamer: Outliers : 2.31 % Allowed : 20.63 % Favored : 77.05 % 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 are not related in a simple way. whole: -1.28 (0.14), residues: 3800 helix: 0.81 (0.12), residues: 1882 sheet: -2.46 (0.25), residues: 368 loop : -2.60 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 108 TYR 0.033 0.001 TYR C 980 PHE 0.036 0.001 PHE A 541 TRP 0.036 0.001 TRP A 887 HIS 0.016 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (31535) covalent geometry : angle 0.72579 / 0.36 (42534) SS BOND : bond 0.00175 / 0.10 ( 10) SS BOND : angle 1.22289 / 0.57 ( 20) hydrogen bonds : bond 0.03034 / 2.02 ( 1236) hydrogen bonds : angle 4.22779 / 2.92 ( 3612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5740.70 seconds wall clock time: 100 minutes 29.91 seconds (6029.91 seconds total)