Starting phenix.real_space_refine on Wed May 28 21:48:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ssa_40749/05_2025/8ssa_40749.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ssa_40749/05_2025/8ssa_40749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ssa_40749/05_2025/8ssa_40749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ssa_40749/05_2025/8ssa_40749.map" model { file = "/net/cci-nas-00/data/ceres_data/8ssa_40749/05_2025/8ssa_40749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ssa_40749/05_2025/8ssa_40749.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 1.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 18.86, per 1000 atoms: 0.61 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: 8.44 Conformation dependent library (CDL) restraints added in 4.0 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: 3.37 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: 11.30 Time building geometry restraints manager: 9.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5004 1.31 - 1.44: 8592 1.44 - 1.57: 17645 1.57 - 1.69: 26 1.69 - 1.82: 268 Bond restraints: 31535 Sorted by residual: bond pdb=" C31 PCW C1101 " pdb=" O2 PCW C1101 " ideal model delta sigma weight residual 1.333 1.423 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C11 PCW A1103 " pdb=" O3 PCW A1103 " ideal model delta sigma weight residual 1.326 1.416 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C31 PCW A1101 " pdb=" O2 PCW A1101 " ideal model delta sigma weight residual 1.333 1.422 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C11 PCW C1103 " pdb=" O3 PCW C1103 " ideal model delta sigma weight residual 1.326 1.415 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C31 PCW D1102 " pdb=" O2 PCW D1102 " ideal model delta sigma weight residual 1.333 1.421 -0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 31530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 40894 2.91 - 5.82: 1292 5.82 - 8.74: 259 8.74 - 11.65: 66 11.65 - 14.56: 23 Bond angle restraints: 42534 Sorted by residual: angle pdb=" C THR B 383 " pdb=" N GLU B 384 " pdb=" CA GLU B 384 " ideal model delta sigma weight residual 121.54 136.10 -14.56 1.91e+00 2.74e-01 5.81e+01 angle pdb=" C THR D 383 " pdb=" N GLU D 384 " pdb=" CA GLU D 384 " ideal model delta sigma weight residual 121.54 136.10 -14.56 1.91e+00 2.74e-01 5.81e+01 angle pdb=" N THR B 383 " pdb=" CA THR B 383 " pdb=" C THR B 383 " ideal model delta sigma weight residual 110.53 102.54 7.99 1.29e+00 6.01e-01 3.84e+01 angle pdb=" N THR D 383 " pdb=" CA THR D 383 " pdb=" C THR D 383 " ideal model delta sigma weight residual 110.53 102.55 7.98 1.29e+00 6.01e-01 3.83e+01 angle pdb=" C ASP A 378 " pdb=" N LYS A 379 " pdb=" CA LYS A 379 " ideal model delta sigma weight residual 121.54 132.73 -11.19 1.91e+00 2.74e-01 3.43e+01 ... (remaining 42529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 18350 35.38 - 70.77: 362 70.77 - 106.15: 37 106.15 - 141.53: 6 141.53 - 176.92: 10 Dihedral angle restraints: 18765 sinusoidal: 7683 harmonic: 11082 Sorted by residual: dihedral pdb=" CA SER A 403 " pdb=" C SER A 403 " pdb=" N PRO A 404 " pdb=" CA PRO A 404 " ideal model delta harmonic sigma weight residual -180.00 -120.26 -59.74 0 5.00e+00 4.00e-02 1.43e+02 dihedral pdb=" CA SER C 403 " pdb=" C SER C 403 " pdb=" N PRO C 404 " pdb=" CA PRO C 404 " ideal model delta harmonic sigma weight residual 180.00 -120.27 -59.73 0 5.00e+00 4.00e-02 1.43e+02 dihedral pdb=" CA SER D 403 " pdb=" C SER D 403 " pdb=" N PRO D 404 " pdb=" CA PRO D 404 " ideal model delta harmonic sigma weight residual -180.00 -125.12 -54.88 0 5.00e+00 4.00e-02 1.20e+02 ... (remaining 18762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3617 0.070 - 0.140: 931 0.140 - 0.210: 107 0.210 - 0.280: 21 0.280 - 0.350: 6 Chirality restraints: 4682 Sorted by residual: chirality pdb=" CB VAL B 395 " pdb=" CA VAL B 395 " pdb=" CG1 VAL B 395 " pdb=" CG2 VAL B 395 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CB VAL D 395 " pdb=" CA VAL D 395 " pdb=" CG1 VAL D 395 " pdb=" CG2 VAL D 395 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB ILE D 459 " pdb=" CA ILE D 459 " pdb=" CG1 ILE D 459 " pdb=" CG2 ILE D 459 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 4679 not shown) Planarity restraints: 5306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 716 " 0.089 5.00e-02 4.00e+02 1.35e-01 2.93e+01 pdb=" N PRO D 717 " -0.234 5.00e-02 4.00e+02 pdb=" CA PRO D 717 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO D 717 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 716 " -0.089 5.00e-02 4.00e+02 1.35e-01 2.92e+01 pdb=" N PRO B 717 " 0.234 5.00e-02 4.00e+02 pdb=" CA PRO B 717 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 717 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 403 " 0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO B 404 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 404 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 404 " 0.048 5.00e-02 4.00e+02 ... (remaining 5303 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4641 2.75 - 3.29: 30159 3.29 - 3.83: 52392 3.83 - 4.36: 62131 4.36 - 4.90: 101578 Nonbonded interactions: 250901 Sorted by model distance: nonbonded pdb=" OH TYR D 128 " pdb=" OG SER D 243 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR B 128 " pdb=" OG SER B 243 " model vdw 2.213 3.040 nonbonded pdb=" O ASP D 490 " pdb=" OG1 THR D 736 " model vdw 2.239 3.040 nonbonded pdb=" O ASP B 490 " pdb=" OG1 THR B 736 " model vdw 2.240 3.040 nonbonded pdb=" OE2 GLU A 25 " pdb=" OG1 THR A 281 " model vdw 2.267 3.040 ... (remaining 250896 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 10 through 821 or resid 1101 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: 3.640 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: 0.030 Extract box with map and model: 1.340 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 68.950 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.150 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.105 31545 Z= 0.462 Angle : 1.318 14.561 42554 Z= 0.672 Chirality : 0.062 0.350 4682 Planarity : 0.008 0.135 5306 Dihedral : 14.930 176.918 11647 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 1.00 % Allowed : 11.37 % Favored : 87.63 % Rotamer: Outliers : 1.00 % Allowed : 6.33 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 5.77 % Twisted General : 0.92 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.037 0.004 TRP A 130 HIS 0.015 0.004 HIS A 214 PHE 0.037 0.004 PHE C 133 TYR 0.034 0.003 TYR E 149 ARG 0.008 0.001 ARG B 715 Details of bonding type rmsd hydrogen bonds : bond 0.28342 ( 1236) hydrogen bonds : angle 9.93656 ( 3612) SS BOND : bond 0.00918 ( 10) SS BOND : angle 1.08789 ( 20) covalent geometry : bond 0.01000 (31535) covalent geometry : angle 1.31812 (42534) *********************** 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 : 3.581 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: 0.4292 time to fit residues: 516.4227 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 : 3.194 ------------------------------------------------------------------------------- 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 322 optimal weight: 7.9990 chunk 289 optimal weight: 0.0870 chunk 160 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 195 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 299 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 346 optimal weight: 10.0000 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 274 HIS A 318 ASN A 337 GLN A 344 ASN ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN A 920 ASN B 10 ASN B 46 HIS B 54 ASN B 164 ASN B 214 HIS B 318 ASN B 335 GLN B 337 GLN B 344 ASN B 392 GLN B 411 ASN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN C 10 ASN C 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.154843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.122936 restraints weight = 74861.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.119515 restraints weight = 70939.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.120461 restraints weight = 47558.070| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31545 Z= 0.163 Angle : 0.756 10.512 42554 Z= 0.397 Chirality : 0.044 0.169 4682 Planarity : 0.006 0.093 5306 Dihedral : 14.752 178.591 4593 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.76 % Favored : 89.82 % Rotamer: Outliers : 2.98 % Allowed : 11.35 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.12), residues: 3800 helix: -1.49 (0.10), residues: 1894 sheet: -2.78 (0.25), residues: 338 loop : -3.17 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 460 HIS 0.006 0.001 HIS C 412 PHE 0.040 0.002 PHE A 965 TYR 0.027 0.002 TYR C 980 ARG 0.006 0.001 ARG E 108 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 1236) hydrogen bonds : angle 5.16080 ( 3612) SS BOND : bond 0.00834 ( 10) SS BOND : angle 1.34461 ( 20) covalent geometry : bond 0.00354 (31535) covalent geometry : angle 0.75537 (42534) *********************** 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 590 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 492 time to evaluate : 3.261 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: A 518 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8468 (pp) REVERT: A 852 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7926 (pt) REVERT: A 938 PHE cc_start: 0.8224 (m-80) cc_final: 0.7905 (m-10) REVERT: A 1000 ASN cc_start: 0.6753 (m-40) cc_final: 0.6471 (m-40) REVERT: A 1022 VAL cc_start: 0.9037 (m) cc_final: 0.8791 (p) REVERT: B 140 ASP cc_start: 0.5918 (t70) cc_final: 0.5065 (t70) REVERT: B 408 MET cc_start: 0.6621 (tmm) cc_final: 0.6227 (tmm) REVERT: B 669 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8826 (ptpp) REVERT: B 673 TYR cc_start: 0.7229 (m-80) cc_final: 0.6954 (m-80) REVERT: B 683 VAL cc_start: 0.7192 (OUTLIER) cc_final: 0.5041 (m) REVERT: B 695 LYS cc_start: 0.8169 (mmpt) cc_final: 0.7579 (tptt) REVERT: B 713 GLU cc_start: 0.8907 (tt0) cc_final: 0.8496 (tt0) REVERT: B 788 SER cc_start: 0.8329 (p) cc_final: 0.8095 (p) REVERT: C 71 TYR cc_start: 0.4267 (m-80) cc_final: 0.4018 (m-80) REVERT: C 518 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8533 (pp) REVERT: C 852 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7822 (pt) REVERT: C 1000 ASN cc_start: 0.6768 (m-40) cc_final: 0.6477 (m-40) REVERT: C 1022 VAL cc_start: 0.9128 (m) cc_final: 0.8793 (p) REVERT: D 138 ASP cc_start: 0.7379 (t0) cc_final: 0.7165 (t0) REVERT: D 140 ASP cc_start: 0.5577 (t70) cc_final: 0.4694 (t70) REVERT: D 669 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8883 (ptpp) REVERT: D 673 TYR cc_start: 0.7204 (m-80) cc_final: 0.6776 (m-80) REVERT: D 695 LYS cc_start: 0.8246 (mmmt) cc_final: 0.7694 (tptt) REVERT: D 711 TYR cc_start: 0.7940 (t80) cc_final: 0.7605 (t80) REVERT: E 5 PHE cc_start: 0.8941 (t80) cc_final: 0.8731 (t80) REVERT: E 101 HIS cc_start: 0.5384 (m-70) cc_final: 0.5054 (m-70) REVERT: E 123 MET cc_start: 0.4145 (mmm) cc_final: 0.3440 (mmm) REVERT: E 126 ASP cc_start: 0.6808 (p0) cc_final: 0.6593 (p0) REVERT: E 144 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6337 (tt) REVERT: F 123 MET cc_start: 0.3959 (mmm) cc_final: 0.3495 (mmm) outliers start: 98 outliers final: 40 residues processed: 564 average time/residue: 0.4081 time to fit residues: 369.5565 Evaluate side-chains 408 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 360 time to evaluate : 3.502 ------------------------------------------------------------------------------- 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 600 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 720 THR 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 B residue 683 VAL 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 110 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 D residue 708 MET Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 83 LEU 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 97 optimal weight: 7.9990 chunk 217 optimal weight: 9.9990 chunk 247 optimal weight: 0.8980 chunk 127 optimal weight: 30.0000 chunk 302 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 181 optimal weight: 0.6980 chunk 224 optimal weight: 7.9990 chunk 242 optimal weight: 6.9990 chunk 23 optimal weight: 0.0970 chunk 87 optimal weight: 9.9990 overall best weight: 2.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 274 HIS B 355 ASN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS D 587 GLN ** 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 = 0.4384 r_free = 0.4384 target = 0.152299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.120990 restraints weight = 75078.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.116890 restraints weight = 76354.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.116867 restraints weight = 54574.618| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31545 Z= 0.197 Angle : 0.751 15.680 42554 Z= 0.387 Chirality : 0.045 0.250 4682 Planarity : 0.005 0.083 5306 Dihedral : 14.066 179.221 4588 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.79 % Favored : 88.82 % Rotamer: Outliers : 3.23 % Allowed : 13.88 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.70 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.13), residues: 3800 helix: -0.58 (0.11), residues: 1898 sheet: -2.64 (0.24), residues: 380 loop : -2.93 (0.14), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 460 HIS 0.028 0.002 HIS C 274 PHE 0.031 0.002 PHE A 965 TYR 0.029 0.002 TYR C 980 ARG 0.006 0.001 ARG E 108 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 1236) hydrogen bonds : angle 4.69869 ( 3612) SS BOND : bond 0.00537 ( 10) SS BOND : angle 1.09599 ( 20) covalent geometry : bond 0.00444 (31535) covalent geometry : angle 0.75050 (42534) *********************** 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 507 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 401 time to evaluate : 3.555 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: A 143 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9225 (mp) REVERT: A 518 LEU cc_start: 0.8918 (pp) cc_final: 0.8613 (pp) REVERT: A 647 TYR cc_start: 0.8011 (p90) cc_final: 0.7775 (p90) REVERT: A 852 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7921 (pt) REVERT: A 1000 ASN cc_start: 0.6630 (m-40) cc_final: 0.6179 (m-40) REVERT: A 1022 VAL cc_start: 0.9015 (m) cc_final: 0.8737 (p) REVERT: B 111 ILE cc_start: 0.7507 (mp) cc_final: 0.7289 (mm) REVERT: B 138 ASP cc_start: 0.7521 (t0) cc_final: 0.7291 (t0) REVERT: B 140 ASP cc_start: 0.6116 (t70) cc_final: 0.5910 (t0) REVERT: B 231 ASP cc_start: 0.7439 (t70) cc_final: 0.7194 (p0) REVERT: B 673 TYR cc_start: 0.7451 (m-80) cc_final: 0.7241 (m-80) REVERT: B 683 VAL cc_start: 0.6954 (OUTLIER) cc_final: 0.5401 (m) REVERT: B 695 LYS cc_start: 0.8131 (mmpt) cc_final: 0.7741 (tptt) REVERT: B 789 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8758 (tt) REVERT: C 74 PHE cc_start: 0.7920 (t80) cc_final: 0.7715 (t80) REVERT: C 518 LEU cc_start: 0.8958 (pp) cc_final: 0.8649 (pp) REVERT: C 647 TYR cc_start: 0.8068 (p90) cc_final: 0.7865 (p90) REVERT: C 852 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7847 (pt) REVERT: C 1000 ASN cc_start: 0.6595 (m-40) cc_final: 0.6151 (m-40) REVERT: C 1022 VAL cc_start: 0.9040 (m) cc_final: 0.8740 (p) REVERT: D 111 ILE cc_start: 0.7842 (mp) cc_final: 0.7522 (mm) REVERT: D 113 MET cc_start: 0.7843 (mpp) cc_final: 0.7411 (mpp) REVERT: D 140 ASP cc_start: 0.5712 (t70) cc_final: 0.4915 (t70) REVERT: D 669 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8954 (ptpp) REVERT: D 695 LYS cc_start: 0.8290 (mmmt) cc_final: 0.7840 (tptt) REVERT: D 788 SER cc_start: 0.8455 (p) cc_final: 0.8177 (t) REVERT: D 789 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8717 (tt) REVERT: E 123 MET cc_start: 0.4379 (mmm) cc_final: 0.3704 (mmm) REVERT: E 126 ASP cc_start: 0.6967 (p0) cc_final: 0.6762 (p0) REVERT: E 144 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6319 (tt) REVERT: F 17 CYS cc_start: 0.7354 (m) cc_final: 0.6953 (m) REVERT: F 123 MET cc_start: 0.4251 (mmm) cc_final: 0.3770 (mmm) outliers start: 106 outliers final: 56 residues processed: 481 average time/residue: 0.3895 time to fit residues: 306.6756 Evaluate side-chains 405 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 341 time to evaluate : 3.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain 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 306 ILE Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 415 LEU 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 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 967 ILE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 33 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 303 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 296 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 343 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 HIS ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN D 355 ASN ** D 412 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.146778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.114556 restraints weight = 75930.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.108281 restraints weight = 83926.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.106210 restraints weight = 64566.316| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 31545 Z= 0.352 Angle : 0.878 14.193 42554 Z= 0.454 Chirality : 0.050 0.268 4682 Planarity : 0.006 0.081 5306 Dihedral : 14.220 168.038 4586 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.76 % Favored : 86.92 % Rotamer: Outliers : 4.38 % Allowed : 15.64 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.65 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.13), residues: 3800 helix: -0.48 (0.12), residues: 1900 sheet: -2.90 (0.23), residues: 416 loop : -3.01 (0.14), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 460 HIS 0.007 0.002 HIS B 214 PHE 0.026 0.003 PHE C 515 TYR 0.032 0.003 TYR D 673 ARG 0.012 0.001 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 1236) hydrogen bonds : angle 5.02746 ( 3612) SS BOND : bond 0.00839 ( 10) SS BOND : angle 1.40033 ( 20) covalent geometry : bond 0.00793 (31535) covalent geometry : angle 0.87805 (42534) *********************** 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 515 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 371 time to evaluate : 3.411 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: A 382 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7686 (tm) REVERT: A 518 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8944 (pp) REVERT: A 585 MET cc_start: 0.8869 (mmm) cc_final: 0.8544 (mtt) REVERT: A 852 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8000 (pt) REVERT: B 111 ILE cc_start: 0.8059 (mp) cc_final: 0.7810 (mm) REVERT: B 138 ASP cc_start: 0.7858 (t0) cc_final: 0.7641 (t0) REVERT: B 231 ASP cc_start: 0.7647 (t0) cc_final: 0.7225 (p0) REVERT: B 419 GLU cc_start: 0.6729 (tp30) cc_final: 0.6395 (tm-30) REVERT: B 449 LYS cc_start: 0.7245 (mmmt) cc_final: 0.6133 (tmtt) REVERT: B 476 ILE cc_start: 0.4603 (OUTLIER) cc_final: 0.4282 (pt) REVERT: B 695 LYS cc_start: 0.8298 (mmpt) cc_final: 0.7892 (tptt) REVERT: B 789 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9078 (tt) REVERT: C 382 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7726 (tm) REVERT: C 518 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8963 (pp) REVERT: C 852 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7987 (pt) REVERT: D 111 ILE cc_start: 0.8001 (mp) cc_final: 0.7752 (mm) REVERT: D 113 MET cc_start: 0.8029 (mpp) cc_final: 0.7775 (mpp) REVERT: D 140 ASP cc_start: 0.5562 (t70) cc_final: 0.5356 (t0) REVERT: D 419 GLU cc_start: 0.6880 (tp30) cc_final: 0.6349 (tm-30) REVERT: D 476 ILE cc_start: 0.4834 (OUTLIER) cc_final: 0.4565 (pt) REVERT: D 673 TYR cc_start: 0.7745 (m-80) cc_final: 0.7536 (m-80) REVERT: D 695 LYS cc_start: 0.8383 (mmmt) cc_final: 0.7949 (tptt) REVERT: D 789 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9107 (tt) REVERT: E 11 MET cc_start: 0.8577 (mtt) cc_final: 0.8258 (mtt) REVERT: E 123 MET cc_start: 0.4766 (mmm) cc_final: 0.4080 (mmm) REVERT: F 17 CYS cc_start: 0.7764 (m) cc_final: 0.7408 (m) REVERT: F 123 MET cc_start: 0.4638 (mmm) cc_final: 0.4113 (mmm) outliers start: 144 outliers final: 85 residues processed: 477 average time/residue: 0.3808 time to fit residues: 303.6750 Evaluate side-chains 418 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 323 time to evaluate : 3.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 165 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 454 ASP Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 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 683 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 784 THR Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 854 ILE 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 1007 PHE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 703 LEU 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 274 HIS Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 401 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 479 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 577 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 683 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 901 PHE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 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 707 THR Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 8 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 142 optimal weight: 6.9990 chunk 212 optimal weight: 0.9980 chunk 203 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 320 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN A 435 HIS B 147 GLN ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN B 355 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN D 355 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** E 132 GLN ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.151888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.121538 restraints weight = 75334.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.115178 restraints weight = 76737.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.116270 restraints weight = 59620.590| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31545 Z= 0.146 Angle : 0.709 15.035 42554 Z= 0.363 Chirality : 0.044 0.194 4682 Planarity : 0.005 0.075 5306 Dihedral : 13.398 166.015 4585 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.63 % Favored : 90.26 % Rotamer: Outliers : 2.74 % Allowed : 18.32 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.13), residues: 3800 helix: 0.01 (0.12), residues: 1896 sheet: -2.75 (0.25), residues: 344 loop : -2.85 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 323 HIS 0.005 0.001 HIS E 27 PHE 0.024 0.002 PHE A 965 TYR 0.035 0.002 TYR B 673 ARG 0.006 0.001 ARG A 178 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 1236) hydrogen bonds : angle 4.40964 ( 3612) SS BOND : bond 0.00692 ( 10) SS BOND : angle 1.07677 ( 20) covalent geometry : bond 0.00328 (31535) covalent geometry : angle 0.70884 (42534) *********************** 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 486 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 396 time to evaluate : 3.611 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: A 382 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7676 (tm) REVERT: A 518 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8514 (pp) REVERT: A 852 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7861 (pt) REVERT: B 76 PHE cc_start: 0.5558 (OUTLIER) cc_final: 0.5283 (m-80) REVERT: B 111 ILE cc_start: 0.7648 (mp) cc_final: 0.7419 (mm) REVERT: B 138 ASP cc_start: 0.7610 (t0) cc_final: 0.7400 (t0) REVERT: B 140 ASP cc_start: 0.5686 (t70) cc_final: 0.5405 (t0) REVERT: B 231 ASP cc_start: 0.7329 (t0) cc_final: 0.7086 (p0) REVERT: B 476 ILE cc_start: 0.4222 (OUTLIER) cc_final: 0.3840 (pt) REVERT: B 695 LYS cc_start: 0.8062 (mmpt) cc_final: 0.7827 (tptt) REVERT: B 732 TYR cc_start: 0.6375 (OUTLIER) cc_final: 0.5851 (m-80) REVERT: B 789 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8758 (tt) REVERT: C 382 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7738 (tm) REVERT: C 518 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8503 (pp) REVERT: C 852 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7822 (pt) REVERT: C 864 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6814 (mt) REVERT: D 113 MET cc_start: 0.7734 (mpp) cc_final: 0.7427 (mpp) REVERT: D 476 ILE cc_start: 0.4469 (OUTLIER) cc_final: 0.4139 (pt) REVERT: D 479 LEU cc_start: 0.7455 (tt) cc_final: 0.7238 (mt) REVERT: D 695 LYS cc_start: 0.8141 (mmmt) cc_final: 0.7868 (tptt) REVERT: D 788 SER cc_start: 0.8509 (p) cc_final: 0.8212 (t) REVERT: D 789 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8762 (tt) REVERT: E 11 MET cc_start: 0.8400 (mtt) cc_final: 0.8102 (mtt) REVERT: E 123 MET cc_start: 0.4587 (mmm) cc_final: 0.3972 (mmm) REVERT: F 123 MET cc_start: 0.4524 (mmm) cc_final: 0.4138 (mmm) outliers start: 90 outliers final: 52 residues processed: 461 average time/residue: 0.3736 time to fit residues: 287.2031 Evaluate side-chains 409 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 344 time to evaluate : 3.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 619 ASN 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 63 CYS Chi-restraints excluded: chain B residue 76 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 428 LEU Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU 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 180 LEU 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 518 LEU Chi-restraints excluded: chain C residue 619 ASN 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 784 THR 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 88 PHE Chi-restraints excluded: chain D residue 233 LEU 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 476 ILE 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 789 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 153 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 321 optimal weight: 6.9990 chunk 247 optimal weight: 0.9990 chunk 379 optimal weight: 20.0000 chunk 189 optimal weight: 0.9990 chunk 108 optimal weight: 0.0970 chunk 316 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN B 355 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN ** E 94 ASN ** 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 = 0.4337 r_free = 0.4337 target = 0.148474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.118272 restraints weight = 75625.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.114497 restraints weight = 85338.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.112951 restraints weight = 67387.233| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 31545 Z= 0.255 Angle : 0.781 14.382 42554 Z= 0.401 Chirality : 0.047 0.190 4682 Planarity : 0.005 0.074 5306 Dihedral : 13.459 161.472 4585 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.34 % Favored : 87.45 % Rotamer: Outliers : 3.93 % Allowed : 18.53 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.13), residues: 3800 helix: 0.06 (0.12), residues: 1892 sheet: -2.72 (0.25), residues: 370 loop : -2.87 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 887 HIS 0.005 0.001 HIS B 214 PHE 0.030 0.002 PHE E 5 TYR 0.034 0.002 TYR C 980 ARG 0.004 0.001 ARG A 309 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 1236) hydrogen bonds : angle 4.59360 ( 3612) SS BOND : bond 0.00308 ( 10) SS BOND : angle 1.05947 ( 20) covalent geometry : bond 0.00578 (31535) covalent geometry : angle 0.78078 (42534) *********************** 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 476 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 347 time to evaluate : 3.755 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: A 382 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7736 (tm) REVERT: A 518 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8738 (pp) REVERT: A 852 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7848 (pt) REVERT: A 864 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7072 (mt) REVERT: B 111 ILE cc_start: 0.7721 (mp) cc_final: 0.7491 (mm) REVERT: B 138 ASP cc_start: 0.7871 (t0) cc_final: 0.7630 (t0) REVERT: B 231 ASP cc_start: 0.7328 (t0) cc_final: 0.7028 (p0) REVERT: B 476 ILE cc_start: 0.4325 (OUTLIER) cc_final: 0.3948 (pt) REVERT: B 695 LYS cc_start: 0.8034 (mmpt) cc_final: 0.7767 (tptt) REVERT: B 732 TYR cc_start: 0.6188 (OUTLIER) cc_final: 0.5556 (m-80) REVERT: B 789 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8907 (tt) REVERT: C 382 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7719 (tm) REVERT: C 518 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8756 (pp) REVERT: C 852 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7827 (pt) REVERT: C 864 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6966 (mt) REVERT: D 476 ILE cc_start: 0.4449 (OUTLIER) cc_final: 0.4171 (pt) REVERT: D 521 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8618 (mp) REVERT: D 695 LYS cc_start: 0.8054 (mmmt) cc_final: 0.7826 (tptt) REVERT: D 783 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.6984 (ptpp) REVERT: D 788 SER cc_start: 0.8498 (OUTLIER) cc_final: 0.8273 (t) REVERT: D 789 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8886 (tt) REVERT: E 11 MET cc_start: 0.8458 (mtt) cc_final: 0.8153 (mtt) REVERT: E 123 MET cc_start: 0.4680 (mmm) cc_final: 0.4093 (mmm) REVERT: F 123 MET cc_start: 0.4691 (mmm) cc_final: 0.4277 (mmm) outliers start: 129 outliers final: 75 residues processed: 445 average time/residue: 0.3720 time to fit residues: 277.7879 Evaluate side-chains 412 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 321 time to evaluate : 3.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 530 VAL 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 683 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain 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 306 ILE Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 685 THR 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 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 518 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 683 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 788 SER 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 D residue 88 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 521 LEU 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 783 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 69 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain F residue 83 LEU 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 54 optimal weight: 0.9990 chunk 240 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 chunk 319 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 107 optimal weight: 0.3980 chunk 293 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 chunk 378 optimal weight: 9.9990 chunk 292 optimal weight: 0.7980 chunk 357 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 HIS B 355 ASN C 214 HIS ** D 112 GLN ** 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 = 0.4397 r_free = 0.4397 target = 0.153233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.123578 restraints weight = 75417.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.119079 restraints weight = 74532.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.118412 restraints weight = 55047.350| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31545 Z= 0.124 Angle : 0.691 14.511 42554 Z= 0.351 Chirality : 0.043 0.195 4682 Planarity : 0.004 0.078 5306 Dihedral : 12.755 160.719 4585 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.79 % Favored : 91.11 % Rotamer: Outliers : 2.31 % Allowed : 20.45 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.14), residues: 3800 helix: 0.48 (0.12), residues: 1898 sheet: -2.58 (0.25), residues: 360 loop : -2.78 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 887 HIS 0.005 0.001 HIS F 75 PHE 0.025 0.001 PHE E 5 TYR 0.031 0.001 TYR C 980 ARG 0.004 0.000 ARG A 675 Details of bonding type rmsd hydrogen bonds : bond 0.03092 ( 1236) hydrogen bonds : angle 4.15775 ( 3612) SS BOND : bond 0.00296 ( 10) SS BOND : angle 1.01310 ( 20) covalent geometry : bond 0.00272 (31535) covalent geometry : angle 0.69044 (42534) *********************** 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 479 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 403 time to evaluate : 3.624 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: A 382 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7780 (tm) REVERT: A 427 ASP cc_start: 0.8591 (m-30) cc_final: 0.8352 (t0) REVERT: A 518 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8408 (pp) REVERT: A 852 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7755 (pt) REVERT: B 111 ILE cc_start: 0.7617 (mp) cc_final: 0.7357 (mm) REVERT: B 138 ASP cc_start: 0.7810 (t0) cc_final: 0.7567 (t0) REVERT: B 476 ILE cc_start: 0.4272 (OUTLIER) cc_final: 0.3876 (pt) REVERT: B 544 SER cc_start: 0.8206 (m) cc_final: 0.7964 (t) REVERT: B 732 TYR cc_start: 0.5911 (OUTLIER) cc_final: 0.5289 (m-80) REVERT: B 788 SER cc_start: 0.8394 (p) cc_final: 0.8081 (m) REVERT: B 789 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8614 (tt) REVERT: C 382 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7873 (tm) REVERT: C 518 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8450 (pp) REVERT: C 852 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7708 (pt) REVERT: D 138 ASP cc_start: 0.7466 (t0) cc_final: 0.7063 (t0) REVERT: D 476 ILE cc_start: 0.4203 (OUTLIER) cc_final: 0.3881 (pt) REVERT: D 479 LEU cc_start: 0.7475 (mt) cc_final: 0.6808 (mp) REVERT: D 695 LYS cc_start: 0.8034 (mmmt) cc_final: 0.7814 (tptt) REVERT: D 789 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8711 (tt) REVERT: E 123 MET cc_start: 0.4603 (mmm) cc_final: 0.4032 (mmm) REVERT: F 11 MET cc_start: 0.8424 (mtm) cc_final: 0.7833 (mtt) REVERT: F 123 MET cc_start: 0.4434 (mmm) cc_final: 0.4098 (mmm) outliers start: 76 outliers final: 43 residues processed: 456 average time/residue: 0.3747 time to fit residues: 286.4480 Evaluate side-chains 407 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 353 time to evaluate : 3.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 619 ASN 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 889 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 309 ARG Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 THR 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 518 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 D residue 88 PHE Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 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 E residue 115 VAL Chi-restraints excluded: chain F residue 83 LEU 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 374 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 278 optimal weight: 7.9990 chunk 248 optimal weight: 0.9990 chunk 313 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 206 optimal weight: 0.6980 chunk 265 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS B 224 ASN B 355 ASN C 412 HIS ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN ** E 94 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.149765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.119508 restraints weight = 75631.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.115907 restraints weight = 82867.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.114139 restraints weight = 60668.361| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 31545 Z= 0.213 Angle : 0.745 14.313 42554 Z= 0.379 Chirality : 0.046 0.208 4682 Planarity : 0.005 0.070 5306 Dihedral : 12.813 162.401 4585 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.26 % Favored : 88.63 % Rotamer: Outliers : 3.04 % Allowed : 20.48 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.14), residues: 3800 helix: 0.48 (0.12), residues: 1890 sheet: -2.54 (0.26), residues: 362 loop : -2.73 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 887 HIS 0.015 0.002 HIS C 412 PHE 0.020 0.002 PHE F 146 TYR 0.044 0.002 TYR D 673 ARG 0.008 0.001 ARG C 675 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 1236) hydrogen bonds : angle 4.32464 ( 3612) SS BOND : bond 0.00211 ( 10) SS BOND : angle 1.06734 ( 20) covalent geometry : bond 0.00487 (31535) covalent geometry : angle 0.74466 (42534) *********************** 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 442 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 342 time to evaluate : 3.739 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: A 382 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7824 (tm) REVERT: A 408 MET cc_start: 0.7695 (tpp) cc_final: 0.6627 (ttt) REVERT: A 518 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8754 (pp) REVERT: A 852 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7924 (pt) REVERT: A 880 MET cc_start: 0.7449 (mmm) cc_final: 0.6280 (tpt) REVERT: A 938 PHE cc_start: 0.8083 (m-80) cc_final: 0.7787 (t80) REVERT: B 111 ILE cc_start: 0.7836 (mp) cc_final: 0.7588 (mm) REVERT: B 476 ILE cc_start: 0.4216 (OUTLIER) cc_final: 0.3855 (pt) REVERT: B 732 TYR cc_start: 0.6222 (OUTLIER) cc_final: 0.5636 (m-80) REVERT: B 789 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8868 (tt) REVERT: C 382 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7910 (tm) REVERT: C 408 MET cc_start: 0.7900 (tpp) cc_final: 0.6890 (ttt) REVERT: C 518 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8795 (pp) REVERT: C 585 MET cc_start: 0.8521 (mmt) cc_final: 0.7797 (mmt) REVERT: C 852 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7888 (pt) REVERT: D 138 ASP cc_start: 0.7885 (t0) cc_final: 0.7517 (t0) REVERT: D 667 PHE cc_start: 0.7880 (m-80) cc_final: 0.7657 (m-80) REVERT: D 789 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8940 (tt) REVERT: E 11 MET cc_start: 0.8396 (mtt) cc_final: 0.8145 (mtt) REVERT: E 123 MET cc_start: 0.4699 (mmm) cc_final: 0.4126 (mmm) REVERT: F 11 MET cc_start: 0.8633 (mtm) cc_final: 0.8048 (mtt) REVERT: F 123 MET cc_start: 0.4588 (mmm) cc_final: 0.4223 (mmm) outliers start: 100 outliers final: 62 residues processed: 412 average time/residue: 0.3637 time to fit residues: 256.6234 Evaluate side-chains 397 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 325 time to evaluate : 3.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 443 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 LEU 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 759 LEU Chi-restraints excluded: chain A residue 789 LEU 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 1016 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 710 GLU 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 306 ILE 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 518 LEU Chi-restraints excluded: chain C residue 577 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 889 VAL Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 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 80 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 153 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 354 optimal weight: 5.9990 chunk 309 optimal weight: 0.2980 chunk 49 optimal weight: 6.9990 chunk 355 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 276 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 247 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN B 355 ASN B 587 GLN D 13 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN ** E 94 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.151208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.125476 restraints weight = 75136.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.124033 restraints weight = 81115.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.122007 restraints weight = 62715.436| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.6042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31545 Z= 0.173 Angle : 0.740 14.922 42554 Z= 0.372 Chirality : 0.045 0.290 4682 Planarity : 0.004 0.069 5306 Dihedral : 12.605 159.869 4585 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.97 % Favored : 89.92 % Rotamer: Outliers : 2.47 % Allowed : 21.33 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.88 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3800 helix: 0.61 (0.12), residues: 1892 sheet: -2.54 (0.26), residues: 364 loop : -2.72 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 887 HIS 0.008 0.001 HIS F 107 PHE 0.020 0.002 PHE F 146 TYR 0.034 0.002 TYR C 980 ARG 0.008 0.000 ARG C 675 Details of bonding type rmsd hydrogen bonds : bond 0.03199 ( 1236) hydrogen bonds : angle 4.27403 ( 3612) SS BOND : bond 0.00174 ( 10) SS BOND : angle 1.04968 ( 20) covalent geometry : bond 0.00396 (31535) covalent geometry : angle 0.74006 (42534) *********************** 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 422 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 341 time to evaluate : 3.302 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: A 382 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7846 (tm) REVERT: A 408 MET cc_start: 0.7279 (tpp) cc_final: 0.6658 (ttt) REVERT: A 518 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8590 (pp) REVERT: A 585 MET cc_start: 0.8663 (tpp) cc_final: 0.7983 (mmm) REVERT: A 939 MET cc_start: 0.5436 (ttm) cc_final: 0.5223 (tpt) REVERT: A 1016 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8887 (tp) REVERT: B 111 ILE cc_start: 0.7549 (mp) cc_final: 0.7336 (mm) REVERT: B 476 ILE cc_start: 0.4037 (OUTLIER) cc_final: 0.3666 (pt) REVERT: B 732 TYR cc_start: 0.5476 (OUTLIER) cc_final: 0.4812 (m-80) REVERT: B 783 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6888 (ptpp) REVERT: B 788 SER cc_start: 0.8415 (p) cc_final: 0.8054 (m) REVERT: B 789 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8785 (tt) REVERT: C 382 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7902 (tm) REVERT: C 408 MET cc_start: 0.7554 (tpp) cc_final: 0.6797 (ttt) REVERT: C 518 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8610 (pp) REVERT: C 585 MET cc_start: 0.8385 (mmt) cc_final: 0.7588 (mmt) REVERT: C 852 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7746 (pt) REVERT: D 138 ASP cc_start: 0.7664 (t0) cc_final: 0.7363 (t0) REVERT: D 789 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8807 (tt) REVERT: E 11 MET cc_start: 0.8282 (mtt) cc_final: 0.8044 (mtt) REVERT: E 123 MET cc_start: 0.4705 (mmm) cc_final: 0.4174 (mmm) REVERT: E 143 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7838 (mp) REVERT: F 11 MET cc_start: 0.8410 (mtm) cc_final: 0.7920 (mtt) REVERT: F 123 MET cc_start: 0.4577 (mmm) cc_final: 0.4266 (mmm) outliers start: 81 outliers final: 57 residues processed: 398 average time/residue: 0.3732 time to fit residues: 252.4547 Evaluate side-chains 392 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 323 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 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 889 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 306 ILE 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 518 LEU Chi-restraints excluded: chain C residue 577 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 789 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 165 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 83 LEU 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 118 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 360 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 351 optimal weight: 0.8980 chunk 184 optimal weight: 5.9990 chunk 352 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 293 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 248 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN ** E 94 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.152869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.128361 restraints weight = 75521.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.127824 restraints weight = 88479.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.127467 restraints weight = 60490.870| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.6246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 31545 Z= 0.139 Angle : 0.731 14.391 42554 Z= 0.365 Chirality : 0.045 0.308 4682 Planarity : 0.004 0.065 5306 Dihedral : 12.304 163.214 4585 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.08 % Favored : 89.82 % Rotamer: Outliers : 2.28 % Allowed : 21.97 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.14), residues: 3800 helix: 0.82 (0.12), residues: 1884 sheet: -2.43 (0.26), residues: 360 loop : -2.66 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 887 HIS 0.007 0.001 HIS F 107 PHE 0.024 0.001 PHE A 965 TYR 0.029 0.001 TYR C 980 ARG 0.010 0.000 ARG E 108 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 1236) hydrogen bonds : angle 4.19062 ( 3612) SS BOND : bond 0.00127 ( 10) SS BOND : angle 1.09564 ( 20) covalent geometry : bond 0.00315 (31535) covalent geometry : angle 0.73032 (42534) ********************** 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 433 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 358 time to evaluate : 3.508 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: 0.8167 (OUTLIER) cc_final: 0.7875 (tm) REVERT: A 408 MET cc_start: 0.7025 (tpp) cc_final: 0.6667 (ttt) REVERT: A 518 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8585 (pp) REVERT: A 585 MET cc_start: 0.8742 (tpp) cc_final: 0.7970 (mmm) REVERT: A 1016 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8846 (tp) REVERT: B 111 ILE cc_start: 0.7439 (mp) cc_final: 0.7172 (mm) REVERT: B 138 ASP cc_start: 0.7558 (t0) cc_final: 0.6935 (t0) REVERT: B 476 ILE cc_start: 0.4135 (OUTLIER) cc_final: 0.3724 (pt) REVERT: B 732 TYR cc_start: 0.5223 (OUTLIER) cc_final: 0.4578 (m-80) REVERT: B 783 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7006 (ptpp) REVERT: B 788 SER cc_start: 0.8321 (p) cc_final: 0.8053 (m) REVERT: B 789 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8744 (tt) REVERT: C 159 GLN cc_start: 0.8074 (mt0) cc_final: 0.7855 (tt0) REVERT: C 382 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7850 (tm) REVERT: C 408 MET cc_start: 0.7320 (tpp) cc_final: 0.6695 (ttt) REVERT: C 518 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8606 (pp) REVERT: C 852 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7721 (pt) REVERT: C 1016 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8849 (tp) REVERT: C 1026 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.5738 (m-80) REVERT: D 138 ASP cc_start: 0.7695 (t0) cc_final: 0.7363 (t0) REVERT: D 479 LEU cc_start: 0.7104 (mt) cc_final: 0.6673 (mp) REVERT: D 770 LYS cc_start: 0.0924 (OUTLIER) cc_final: 0.0510 (pmmt) REVERT: D 788 SER cc_start: 0.8244 (p) cc_final: 0.7965 (m) REVERT: D 789 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8763 (tt) REVERT: E 11 MET cc_start: 0.8217 (mtt) cc_final: 0.7926 (mtt) REVERT: E 123 MET cc_start: 0.4763 (mmm) cc_final: 0.4308 (mmm) REVERT: F 11 MET cc_start: 0.8312 (mtm) cc_final: 0.7867 (mtt) REVERT: F 123 MET cc_start: 0.4590 (mmm) cc_final: 0.4355 (mmm) outliers start: 75 outliers final: 53 residues processed: 410 average time/residue: 0.3708 time to fit residues: 257.6776 Evaluate side-chains 392 residues out of total 3286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 325 time to evaluate : 3.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 530 VAL 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 852 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 306 ILE 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 518 LEU Chi-restraints excluded: chain C residue 577 LEU 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 789 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 C residue 1026 TYR Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 770 LYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 83 LEU 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 95 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 321 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 289 optimal weight: 0.0870 chunk 345 optimal weight: 30.0000 chunk 221 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN B 355 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN ** E 94 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.153966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.130189 restraints weight = 75257.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.129209 restraints weight = 88736.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.128781 restraints weight = 64032.011| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.6447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 31545 Z= 0.132 Angle : 0.728 13.933 42554 Z= 0.362 Chirality : 0.044 0.283 4682 Planarity : 0.004 0.068 5306 Dihedral : 12.047 160.998 4583 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.42 % Favored : 90.47 % Rotamer: Outliers : 2.13 % Allowed : 21.91 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 3800 helix: 0.96 (0.12), residues: 1880 sheet: -2.36 (0.26), residues: 360 loop : -2.62 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 887 HIS 0.007 0.001 HIS F 107 PHE 0.027 0.001 PHE A 965 TYR 0.033 0.001 TYR C 980 ARG 0.007 0.000 ARG C 675 Details of bonding type rmsd hydrogen bonds : bond 0.03111 ( 1236) hydrogen bonds : angle 4.12143 ( 3612) SS BOND : bond 0.00186 ( 10) SS BOND : angle 1.32504 ( 20) covalent geometry : bond 0.00297 (31535) covalent geometry : angle 0.72755 (42534) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10045.95 seconds wall clock time: 177 minutes 21.98 seconds (10641.98 seconds total)