Starting phenix.real_space_refine on Sun Aug 24 05:48:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ocf_12806/08_2025/7ocf_12806.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ocf_12806/08_2025/7ocf_12806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ocf_12806/08_2025/7ocf_12806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ocf_12806/08_2025/7ocf_12806.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ocf_12806/08_2025/7ocf_12806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ocf_12806/08_2025/7ocf_12806.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 S 104 5.16 5 Cl 4 4.86 5 C 11320 2.51 5 N 2710 2.21 5 O 2950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17088 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 2803 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 483 Unresolved non-hydrogen dihedrals: 338 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 23, 'ASP:plan': 8, 'ASN:plan1': 2, 'GLN:plan1': 4, 'PHE:plan': 1, 'ARG:plan': 9, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 220 Chain: "B" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2878 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 15, 'PHE:plan': 1, 'ASP:plan': 7, 'TYR:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "G" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1222 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 5, 'GLN:plan1': 2, 'ASN:plan1': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 64 Chain: "I" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1322 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 2, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 5, 'ARG:plan': 2, 'TYR:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 2803 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 483 Unresolved non-hydrogen dihedrals: 338 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 23, 'ASP:plan': 8, 'ASN:plan1': 2, 'GLN:plan1': 4, 'PHE:plan': 1, 'ARG:plan': 9, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 220 Chain: "E" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1222 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 5, 'GLN:plan1': 2, 'ASN:plan1': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 64 Chain: "J" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1322 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 2, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 5, 'ARG:plan': 2, 'TYR:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "D" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2878 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 15, 'PHE:plan': 1, 'ASP:plan': 7, 'TYR:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 147 Unusual residues: {'CYZ': 1, 'PC1': 6} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PC1:plan-2': 6} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 132 Unusual residues: {'CYZ': 1, 'PC1': 5} Classifications: {'peptide': 1, 'undetermined': 6} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PC1:plan-2': 4, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 19 Chain: "I" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 147 Unusual residues: {'CYZ': 1, 'PC1': 6} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PC1:plan-2': 6} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PC1:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 114 Unusual residues: {'CYZ': 1, 'PC1': 4} Classifications: {'peptide': 1, 'undetermined': 5} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 3.34, per 1000 atoms: 0.20 Number of scatterers: 17088 At special positions: 0 Unit cell: (116.63, 112.35, 146.59, 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) Cl 4 17.00 S 104 16.00 O 2950 8.00 N 2710 7.00 C 11320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS I 52 " - pdb=" SG CYS I 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 90 " - pdb=" SG CYS I 100 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS J 52 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 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: 1.68 Conformation dependent library (CDL) restraints added in 654.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4228 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 18 sheets defined 60.2% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.794A pdb=" N LEU A 514 " --> pdb=" O PHE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 541 Processing helix chain 'A' and resid 543 through 548 removed outlier: 3.990A pdb=" N TRP A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 581 Processing helix chain 'A' and resid 591 through 621 removed outlier: 4.090A pdb=" N VAL A 597 " --> pdb=" O SER A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 649 through 658 Processing helix chain 'A' and resid 660 through 672 removed outlier: 4.308A pdb=" N SER A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 703 through 710 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 784 through 815 removed outlier: 4.033A pdb=" N VAL A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLY A 790 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A 791 " --> pdb=" O ASN A 787 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 removed outlier: 3.557A pdb=" N LEU B 415 " --> pdb=" O HIS B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.672A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.738A pdb=" N HIS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 removed outlier: 3.598A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 573 through 585 Processing helix chain 'B' and resid 595 through 618 removed outlier: 4.120A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 618 " --> pdb=" O SER B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 626 Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.641A pdb=" N GLN B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 694 Processing helix chain 'B' and resid 705 through 715 removed outlier: 3.819A pdb=" N ASN B 709 " --> pdb=" O GLU B 705 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 710 " --> pdb=" O SER B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 792 through 819 removed outlier: 4.065A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 40 removed outlier: 3.717A pdb=" N SER G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 85 removed outlier: 3.704A pdb=" N ARG G 53 " --> pdb=" O ARG G 49 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL G 69 " --> pdb=" O ARG G 65 " (cutoff:3.500A) Proline residue: G 70 - end of helix Processing helix chain 'G' and resid 88 through 107 Proline residue: G 96 - end of helix Processing helix chain 'G' and resid 124 through 159 Processing helix chain 'I' and resid 19 through 42 removed outlier: 3.905A pdb=" N LEU I 23 " --> pdb=" O VAL I 19 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP I 42 " --> pdb=" O ALA I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 114 Processing helix chain 'I' and resid 115 through 128 Processing helix chain 'I' and resid 128 through 149 removed outlier: 3.663A pdb=" N ILE I 132 " --> pdb=" O SER I 128 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG I 149 " --> pdb=" O VAL I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 186 removed outlier: 3.638A pdb=" N LEU I 159 " --> pdb=" O ARG I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 233 removed outlier: 3.543A pdb=" N TYR I 206 " --> pdb=" O GLY I 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 511 through 515 removed outlier: 3.800A pdb=" N LEU C 514 " --> pdb=" O PHE C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 541 Processing helix chain 'C' and resid 543 through 548 removed outlier: 3.993A pdb=" N TRP C 547 " --> pdb=" O SER C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 581 Processing helix chain 'C' and resid 591 through 621 removed outlier: 4.083A pdb=" N VAL C 597 " --> pdb=" O SER C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 638 Processing helix chain 'C' and resid 649 through 658 Processing helix chain 'C' and resid 660 through 672 removed outlier: 4.312A pdb=" N SER C 672 " --> pdb=" O THR C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'C' and resid 703 through 710 Processing helix chain 'C' and resid 739 through 752 Processing helix chain 'C' and resid 753 through 764 Processing helix chain 'C' and resid 784 through 815 removed outlier: 4.033A pdb=" N VAL C 788 " --> pdb=" O SER C 784 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLY C 790 " --> pdb=" O SER C 786 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL C 791 " --> pdb=" O ASN C 787 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 40 removed outlier: 3.717A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 85 removed outlier: 3.704A pdb=" N ARG E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 88 through 107 Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 124 through 159 Processing helix chain 'J' and resid 19 through 42 removed outlier: 3.904A pdb=" N LEU J 23 " --> pdb=" O VAL J 19 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP J 42 " --> pdb=" O ALA J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 114 Processing helix chain 'J' and resid 115 through 128 Processing helix chain 'J' and resid 128 through 149 removed outlier: 3.663A pdb=" N ILE J 132 " --> pdb=" O SER J 128 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG J 149 " --> pdb=" O VAL J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 186 removed outlier: 3.638A pdb=" N LEU J 159 " --> pdb=" O ARG J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 233 removed outlier: 3.542A pdb=" N TYR J 206 " --> pdb=" O GLY J 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 removed outlier: 3.557A pdb=" N LEU D 415 " --> pdb=" O HIS D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.672A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.738A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 removed outlier: 3.598A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 573 through 585 Processing helix chain 'D' and resid 595 through 618 removed outlier: 4.120A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA D 618 " --> pdb=" O SER D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 626 Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.642A pdb=" N GLN D 642 " --> pdb=" O ASP D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 694 Processing helix chain 'D' and resid 705 through 715 removed outlier: 3.819A pdb=" N ASN D 709 " --> pdb=" O GLU D 705 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU D 710 " --> pdb=" O SER D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 792 through 819 removed outlier: 4.065A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 486 through 487 Processing sheet with id=AA2, first strand: chain 'A' and resid 493 through 494 Processing sheet with id=AA3, first strand: chain 'A' and resid 642 through 645 removed outlier: 6.352A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 397 through 399 removed outlier: 6.004A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA6, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AA7, first strand: chain 'B' and resid 646 through 649 removed outlier: 8.478A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 80 through 82 Processing sheet with id=AA9, first strand: chain 'I' and resid 88 through 90 Processing sheet with id=AB1, first strand: chain 'C' and resid 486 through 487 Processing sheet with id=AB2, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AB3, first strand: chain 'C' and resid 642 through 645 removed outlier: 6.352A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 80 through 82 Processing sheet with id=AB5, first strand: chain 'J' and resid 88 through 90 Processing sheet with id=AB6, first strand: chain 'D' and resid 397 through 399 removed outlier: 6.003A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AB9, first strand: chain 'D' and resid 646 through 649 removed outlier: 8.478A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) 1036 hydrogen bonds defined for protein. 3048 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: 2.50 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.16: 12 1.16 - 1.33: 3091 1.33 - 1.50: 7476 1.50 - 1.67: 6717 1.67 - 1.83: 166 Bond restraints: 17462 Sorted by residual: bond pdb=" C2 CYZ C1401 " pdb=" C3 CYZ C1401 " ideal model delta sigma weight residual 1.513 0.990 0.523 2.00e-02 2.50e+03 6.83e+02 bond pdb=" C2 CYZ A1401 " pdb=" C3 CYZ A1401 " ideal model delta sigma weight residual 1.513 0.991 0.522 2.00e-02 2.50e+03 6.81e+02 bond pdb=" C2 CYZ B1401 " pdb=" C3 CYZ B1401 " ideal model delta sigma weight residual 1.513 0.996 0.517 2.00e-02 2.50e+03 6.70e+02 bond pdb=" C2 CYZ D1401 " pdb=" C3 CYZ D1401 " ideal model delta sigma weight residual 1.513 0.996 0.517 2.00e-02 2.50e+03 6.69e+02 bond pdb=" C4 CYZ C1401 " pdb=" C5 CYZ C1401 " ideal model delta sigma weight residual 1.512 1.072 0.440 2.00e-02 2.50e+03 4.85e+02 ... (remaining 17457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.11: 23580 5.11 - 10.22: 108 10.22 - 15.33: 0 15.33 - 20.44: 8 20.44 - 25.55: 2 Bond angle restraints: 23698 Sorted by residual: angle pdb=" CD LYS I 102 " pdb=" CE LYS I 102 " pdb=" NZ LYS I 102 " ideal model delta sigma weight residual 111.90 86.35 25.55 3.20e+00 9.77e-02 6.38e+01 angle pdb=" CD LYS J 102 " pdb=" CE LYS J 102 " pdb=" NZ LYS J 102 " ideal model delta sigma weight residual 111.90 86.41 25.49 3.20e+00 9.77e-02 6.35e+01 angle pdb=" O3 CYZ B1401 " pdb=" S2 CYZ B1401 " pdb=" O4 CYZ B1401 " ideal model delta sigma weight residual 118.35 101.03 17.32 3.00e+00 1.11e-01 3.33e+01 angle pdb=" O3 CYZ D1401 " pdb=" S2 CYZ D1401 " pdb=" O4 CYZ D1401 " ideal model delta sigma weight residual 118.35 101.08 17.27 3.00e+00 1.11e-01 3.31e+01 angle pdb=" O3 CYZ C1401 " pdb=" S2 CYZ C1401 " pdb=" O4 CYZ C1401 " ideal model delta sigma weight residual 118.35 101.12 17.23 3.00e+00 1.11e-01 3.30e+01 ... (remaining 23693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 9535 21.78 - 43.55: 511 43.55 - 65.33: 80 65.33 - 87.10: 22 87.10 - 108.88: 10 Dihedral angle restraints: 10158 sinusoidal: 3550 harmonic: 6608 Sorted by residual: dihedral pdb=" N2 CYZ B1401 " pdb=" C8 CYZ B1401 " pdb=" N1 CYZ B1401 " pdb=" S1 CYZ B1401 " ideal model delta sinusoidal sigma weight residual 55.73 -53.15 108.88 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" N2 CYZ D1401 " pdb=" C8 CYZ D1401 " pdb=" N1 CYZ D1401 " pdb=" S1 CYZ D1401 " ideal model delta sinusoidal sigma weight residual 55.73 -53.12 108.85 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C1 CYZ B1401 " pdb=" C8 CYZ B1401 " pdb=" N1 CYZ B1401 " pdb=" S1 CYZ B1401 " ideal model delta sinusoidal sigma weight residual -71.23 -175.51 104.28 1 3.00e+01 1.11e-03 1.33e+01 ... (remaining 10155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.393: 2722 0.393 - 0.785: 8 0.785 - 1.178: 0 1.178 - 1.570: 4 1.570 - 1.963: 4 Chirality restraints: 2738 Sorted by residual: chirality pdb=" C2 CYZ C1401 " pdb=" C1 CYZ C1401 " pdb=" C3 CYZ C1401 " pdb=" C7 CYZ C1401 " both_signs ideal model delta sigma weight residual False 3.31 1.35 1.96 2.00e-01 2.50e+01 9.63e+01 chirality pdb=" C2 CYZ A1401 " pdb=" C1 CYZ A1401 " pdb=" C3 CYZ A1401 " pdb=" C7 CYZ A1401 " both_signs ideal model delta sigma weight residual False 3.31 1.35 1.96 2.00e-01 2.50e+01 9.63e+01 chirality pdb=" C2 CYZ B1401 " pdb=" C1 CYZ B1401 " pdb=" C3 CYZ B1401 " pdb=" C7 CYZ B1401 " both_signs ideal model delta sigma weight residual False 3.31 1.35 1.96 2.00e-01 2.50e+01 9.57e+01 ... (remaining 2735 not shown) Planarity restraints: 2886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 403 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.30e+00 pdb=" N PRO B 404 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 404 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 404 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 403 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO D 404 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 404 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 404 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 399 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO C 400 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 400 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 400 " -0.022 5.00e-02 4.00e+02 ... (remaining 2883 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 159 2.63 - 3.20: 16621 3.20 - 3.77: 25470 3.77 - 4.33: 33810 4.33 - 4.90: 57526 Nonbonded interactions: 133586 Sorted by model distance: nonbonded pdb=" O TYR I 43 " pdb=" OG SER I 204 " model vdw 2.067 3.040 nonbonded pdb=" O TYR J 43 " pdb=" OG SER J 204 " model vdw 2.067 3.040 nonbonded pdb=" N GLU B 705 " pdb=" OE1 GLU B 705 " model vdw 2.095 3.120 nonbonded pdb=" N GLU D 705 " pdb=" OE1 GLU D 705 " model vdw 2.095 3.120 nonbonded pdb=" O GLY C 568 " pdb=" OG SER C 572 " model vdw 2.106 3.040 ... (remaining 133581 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' and ((resid 393 through 398 and (name N or name CA or name C or name \ O or name CB )) or resid 400 through 403 or resid 405 through 407 or resid 412 t \ hrough 414 or resid 416 through 422 or resid 424 through 431 or resid 433 or res \ id 436 or resid 438 or resid 440 through 441 or resid 443 through 450 or (resid \ 452 through 454 and (name N or name CA or name C or name O or name CB )) or resi \ d 456 through 466 or (resid 468 through 469 and (name N or name CA or name C or \ name O or name CB )) or resid 471 or resid 473 through 478 or (resid 479 and (na \ me N or name CA or name C or name O or name CB )) or resid 480 through 485 or (r \ esid 486 and (name N or name CA or name C or name O or name CB )) or resid 487 t \ hrough 544 or (resid 545 through 546 and (name N or name CA or name C or name O \ or name CB )) or resid 567 through 581 or resid 583 through 628 or (resid 629 th \ rough 630 and (name N or name CA or name C or name O or name CB )) or resid 631 \ through 635 or resid 637 through 646 or resid 649 through 656 or (resid 657 and \ (name N or name CA or name C or name O or name CB )) or resid 658 through 663 or \ resid 665 through 668 or (resid 669 through 670 and (name N or name CA or name \ C or name O or name CB )) or resid 672 through 675 or (resid 676 and (name N or \ name CA or name C or name O or name CB )) or resid 677 through 682 or resid 684 \ through 685 or resid 688 through 690 or (resid 691 and (name N or name CA or nam \ e C or name O or name CB )) or resid 692 through 714 or (resid 715 and (name N o \ r name CA or name C or name O or name CB )) or resid 716 through 736 or resid 73 \ 8 or resid 741 or (resid 742 and (name N or name CA or name C or name O or name \ CB )) or resid 743 through 753 or (resid 754 and (name N or name CA or name C or \ name O or name CB )) or resid 755 through 758 or (resid 759 and (name N or name \ CA or name C or name O or name CB )) or resid 761 through 783 or (resid 784 and \ (name N or name CA or name C or name O or name CB )) or resid 785 through 795 o \ r resid 797 through 1401 or (resid 1402 and (name C21 or name C22 or name C23 or \ name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C2 \ A or name C2B or name C2C or name C2D or name C2E or name O21 or name O22)) or r \ esid 1403 through 1404 or resid 1408)) selection = (chain 'B' and ((resid 397 through 402 and (name N or name CA or name C or name \ O or name CB )) or resid 404 through 405 or (resid 406 through 407 and (name N o \ r name CA or name C or name O or name CB )) or (resid 409 through 411 and (name \ N or name CA or name C or name O or name CB )) or resid 416 through 418 or (resi \ d 420 and (name N or name CA or name C or name O or name CB )) or resid 421 or ( \ resid 422 and (name N or name CA or name C or name O or name CB )) or resid 423 \ through 424 or (resid 425 through 426 and (name N or name CA or name C or name O \ or name CB )) or resid 428 through 434 or (resid 435 and (name N or name CA or \ name C or name O or name CB )) or resid 437 or resid 440 or resid 442 or resid 4 \ 44 through 445 or (resid 447 and (name N or name CA or name C or name O or name \ CB )) or resid 448 or (resid 449 and (name N or name CA or name C or name O or n \ ame CB )) or resid 450 through 452 or (resid 453 through 454 and (name N or name \ CA or name C or name O or name CB )) or resid 456 through 458 or resid 460 thro \ ugh 462 or (resid 463 and (name N or name CA or name C or name O or name CB )) o \ r resid 464 through 466 or (resid 467 and (name N or name CA or name C or name O \ or name CB )) or resid 468 through 470 or resid 472 through 473 or resid 475 or \ resid 477 through 480 or (resid 481 and (name N or name CA or name C or name O \ or name CB )) or resid 482 through 504 or (resid 505 through 506 and (name N or \ name CA or name C or name O or name CB )) or resid 507 or (resid 508 through 511 \ and (name N or name CA or name C or name O or name CB )) or resid 512 through 5 \ 85 or resid 587 through 625 or (resid 626 through 631 and (name N or name CA or \ name C or name O or name CB )) or resid 632 through 637 or (resid 638 through 63 \ 9 and (name N or name CA or name C or name O or name CB )) or (resid 641 through \ 642 and (name N or name CA or name C or name O or name CB )) or resid 643 throu \ gh 648 or (resid 649 and (name N or name CA or name C or name O or name CB )) or \ resid 650 or resid 653 through 663 or (resid 664 through 665 and (name N or nam \ e CA or name C or name O or name CB )) or resid 666 through 667 or (resid 669 th \ rough 670 and (name N or name CA or name C or name O or name CB )) or resid 671 \ or (resid 672 through 674 and (name N or name CA or name C or name O or name CB \ )) or (resid 676 through 678 and (name N or name CA or name C or name O or name \ CB )) or resid 679 through 684 or (resid 685 and (name N or name CA or name C or \ name O or name CB )) or resid 686 or resid 688 through 689 or (resid 692 and (n \ ame N or name CA or name C or name O or name CB )) or resid 693 through 704 or ( \ resid 705 and (name N or name CA or name C or name O or name CB )) or resid 706 \ through 712 or (resid 713 and (name N or name CA or name C or name O or name CB \ )) or resid 714 through 739 or (resid 740 and (name N or name CA or name C or na \ me O or name CB )) or (resid 742 and (name N or name CA or name C or name O or n \ ame CB )) or resid 745 through 751 or (resid 752 and (name N or name CA or name \ C or name O or name CB )) or resid 753 through 759 or (resid 760 through 761 and \ (name N or name CA or name C or name O or name CB )) or resid 762 through 763 o \ r (resid 765 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 66 through 774 or (resid 783 and (name N or name CA or name C or name O or name \ CB )) or resid 784 through 799 or resid 801 through 812 or (resid 813 and (name \ N or name CA or name C or name O or name CB )) or resid 814 through 816 or (resi \ d 817 through 819 and (name N or name CA or name C or name O or name CB )) or re \ sid 1401 through 1402 or (resid 1403 through 1404 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G or name O21 or name O22)) or resid 1407)) selection = (chain 'C' and ((resid 393 through 398 and (name N or name CA or name C or name \ O or name CB )) or resid 400 through 403 or resid 405 through 407 or resid 412 t \ hrough 414 or resid 416 through 422 or resid 424 through 431 or resid 433 or res \ id 436 or resid 438 or resid 440 through 441 or resid 443 through 450 or (resid \ 452 through 454 and (name N or name CA or name C or name O or name CB )) or resi \ d 456 through 466 or (resid 468 through 469 and (name N or name CA or name C or \ name O or name CB )) or resid 471 or resid 473 through 478 or (resid 479 and (na \ me N or name CA or name C or name O or name CB )) or resid 480 through 485 or (r \ esid 486 and (name N or name CA or name C or name O or name CB )) or resid 487 t \ hrough 544 or (resid 545 through 546 and (name N or name CA or name C or name O \ or name CB )) or resid 567 through 581 or resid 583 through 628 or (resid 629 th \ rough 630 and (name N or name CA or name C or name O or name CB )) or resid 631 \ through 635 or resid 637 through 646 or resid 649 through 656 or (resid 657 and \ (name N or name CA or name C or name O or name CB )) or resid 658 through 663 or \ resid 665 through 668 or (resid 669 through 670 and (name N or name CA or name \ C or name O or name CB )) or resid 672 through 675 or (resid 676 and (name N or \ name CA or name C or name O or name CB )) or resid 677 through 682 or resid 684 \ through 685 or resid 688 through 690 or (resid 691 and (name N or name CA or nam \ e C or name O or name CB )) or resid 692 through 714 or (resid 715 and (name N o \ r name CA or name C or name O or name CB )) or resid 716 through 736 or resid 73 \ 8 or resid 741 or (resid 742 and (name N or name CA or name C or name O or name \ CB )) or resid 743 through 753 or (resid 754 and (name N or name CA or name C or \ name O or name CB )) or resid 755 through 758 or (resid 759 and (name N or name \ CA or name C or name O or name CB )) or resid 761 through 783 or (resid 784 and \ (name N or name CA or name C or name O or name CB )) or resid 785 through 795 o \ r resid 797 through 1401 or (resid 1402 and (name C21 or name C22 or name C23 or \ name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C2 \ A or name C2B or name C2C or name C2D or name C2E or name O21 or name O22)) or r \ esid 1403 through 1404 or resid 1408)) selection = (chain 'D' and ((resid 397 through 402 and (name N or name CA or name C or name \ O or name CB )) or resid 404 through 405 or (resid 406 through 407 and (name N o \ r name CA or name C or name O or name CB )) or (resid 409 through 411 and (name \ N or name CA or name C or name O or name CB )) or resid 416 through 418 or (resi \ d 420 and (name N or name CA or name C or name O or name CB )) or resid 421 or ( \ resid 422 and (name N or name CA or name C or name O or name CB )) or resid 423 \ through 424 or (resid 425 through 426 and (name N or name CA or name C or name O \ or name CB )) or resid 428 through 434 or (resid 435 and (name N or name CA or \ name C or name O or name CB )) or resid 437 or resid 440 or resid 442 or resid 4 \ 44 through 445 or (resid 447 and (name N or name CA or name C or name O or name \ CB )) or resid 448 or (resid 449 and (name N or name CA or name C or name O or n \ ame CB )) or resid 450 through 452 or (resid 453 through 454 and (name N or name \ CA or name C or name O or name CB )) or resid 456 through 458 or resid 460 thro \ ugh 462 or (resid 463 and (name N or name CA or name C or name O or name CB )) o \ r resid 464 through 466 or (resid 467 and (name N or name CA or name C or name O \ or name CB )) or resid 468 through 470 or resid 472 through 473 or resid 475 or \ resid 477 through 480 or (resid 481 and (name N or name CA or name C or name O \ or name CB )) or resid 482 through 504 or (resid 505 through 506 and (name N or \ name CA or name C or name O or name CB )) or resid 507 or (resid 508 through 511 \ and (name N or name CA or name C or name O or name CB )) or resid 512 through 5 \ 85 or resid 587 through 625 or (resid 626 through 631 and (name N or name CA or \ name C or name O or name CB )) or resid 632 through 637 or (resid 638 through 63 \ 9 and (name N or name CA or name C or name O or name CB )) or (resid 641 through \ 642 and (name N or name CA or name C or name O or name CB )) or resid 643 throu \ gh 648 or (resid 649 and (name N or name CA or name C or name O or name CB )) or \ resid 650 or resid 653 through 663 or (resid 664 through 665 and (name N or nam \ e CA or name C or name O or name CB )) or resid 666 through 667 or (resid 669 th \ rough 670 and (name N or name CA or name C or name O or name CB )) or resid 671 \ or (resid 672 through 674 and (name N or name CA or name C or name O or name CB \ )) or (resid 676 through 678 and (name N or name CA or name C or name O or name \ CB )) or resid 679 through 684 or (resid 685 and (name N or name CA or name C or \ name O or name CB )) or resid 686 or resid 688 through 689 or (resid 692 and (n \ ame N or name CA or name C or name O or name CB )) or resid 693 through 704 or ( \ resid 705 and (name N or name CA or name C or name O or name CB )) or resid 706 \ through 712 or (resid 713 and (name N or name CA or name C or name O or name CB \ )) or resid 714 through 739 or (resid 740 and (name N or name CA or name C or na \ me O or name CB )) or (resid 742 and (name N or name CA or name C or name O or n \ ame CB )) or resid 745 through 751 or (resid 752 and (name N or name CA or name \ C or name O or name CB )) or resid 753 through 759 or (resid 760 through 761 and \ (name N or name CA or name C or name O or name CB )) or resid 762 through 763 o \ r (resid 765 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 66 through 774 or (resid 783 and (name N or name CA or name C or name O or name \ CB )) or resid 784 through 799 or resid 801 through 812 or (resid 813 and (name \ N or name CA or name C or name O or name CB )) or resid 814 through 816 or (resi \ d 817 through 819 and (name N or name CA or name C or name O or name CB )) or re \ sid 1401 through 1402 or (resid 1403 through 1404 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G or name O21 or name O22)) or resid 1406)) } ncs_group { reference = (chain 'E' and resid 2 through 159) selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.910 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 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 : 0.018 0.523 17470 Z= 0.871 Angle : 0.947 25.552 23714 Z= 0.395 Chirality : 0.109 1.963 2738 Planarity : 0.003 0.058 2886 Dihedral : 14.254 108.876 5906 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.18), residues: 2254 helix: 1.48 (0.14), residues: 1302 sheet: -1.34 (0.39), residues: 168 loop : -1.92 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 656 TYR 0.013 0.001 TYR B 616 PHE 0.015 0.002 PHE B 574 TRP 0.009 0.001 TRP C 601 HIS 0.003 0.001 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.01801 (17462) covalent geometry : angle 0.94684 (23698) SS BOND : bond 0.00179 ( 8) SS BOND : angle 0.63111 ( 16) hydrogen bonds : bond 0.12393 ( 1036) hydrogen bonds : angle 5.09933 ( 3048) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 498 ILE cc_start: 0.8015 (mt) cc_final: 0.7806 (mt) REVERT: B 628 ARG cc_start: 0.7156 (pmt-80) cc_final: 0.6929 (pmt-80) REVERT: G 35 ARG cc_start: 0.7824 (ttp-170) cc_final: 0.7314 (ttp-170) REVERT: I 22 LEU cc_start: 0.7948 (tp) cc_final: 0.7599 (mt) REVERT: I 118 GLU cc_start: 0.7676 (tp30) cc_final: 0.7351 (tp30) REVERT: E 9 CYS cc_start: 0.8100 (m) cc_final: 0.7860 (m) REVERT: J 26 ILE cc_start: 0.8398 (mm) cc_final: 0.8125 (mt) REVERT: J 118 GLU cc_start: 0.7747 (tp30) cc_final: 0.7545 (tp30) REVERT: D 407 MET cc_start: 0.6729 (mmm) cc_final: 0.6196 (mtm) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.1333 time to fit residues: 64.9713 Evaluate side-chains 293 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN B 411 ASN C 710 GLN J 183 ASN D 411 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.172839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.116860 restraints weight = 21940.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.115402 restraints weight = 26853.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117179 restraints weight = 22879.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118112 restraints weight = 15428.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118163 restraints weight = 14474.138| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17470 Z= 0.150 Angle : 0.562 8.990 23714 Z= 0.286 Chirality : 0.041 0.177 2738 Planarity : 0.004 0.043 2886 Dihedral : 11.302 91.458 2964 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.14 % Allowed : 9.53 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.18), residues: 2254 helix: 2.02 (0.14), residues: 1326 sheet: -1.36 (0.43), residues: 116 loop : -1.62 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 657 TYR 0.014 0.001 TYR C 669 PHE 0.022 0.001 PHE D 546 TRP 0.020 0.001 TRP B 460 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00350 (17462) covalent geometry : angle 0.56178 (23698) SS BOND : bond 0.00156 ( 8) SS BOND : angle 1.12116 ( 16) hydrogen bonds : bond 0.04208 ( 1036) hydrogen bonds : angle 3.99805 ( 3048) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 324 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 475 LEU cc_start: 0.7870 (tt) cc_final: 0.7653 (tp) REVERT: A 485 ILE cc_start: 0.8736 (tp) cc_final: 0.8348 (tp) REVERT: A 498 ILE cc_start: 0.7952 (mt) cc_final: 0.7726 (mt) REVERT: A 581 MET cc_start: 0.8915 (mmt) cc_final: 0.8559 (mmt) REVERT: G 35 ARG cc_start: 0.7697 (ttp-170) cc_final: 0.7215 (ttp-170) REVERT: I 43 TYR cc_start: 0.7648 (OUTLIER) cc_final: 0.6545 (t80) REVERT: I 102 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8541 (tmmt) REVERT: I 118 GLU cc_start: 0.7906 (tp30) cc_final: 0.7679 (tp30) REVERT: C 475 LEU cc_start: 0.8048 (tt) cc_final: 0.7840 (tp) REVERT: J 26 ILE cc_start: 0.8426 (mm) cc_final: 0.8097 (mt) REVERT: D 405 TYR cc_start: 0.6829 (m-80) cc_final: 0.6622 (m-80) REVERT: D 487 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8229 (mt-10) outliers start: 17 outliers final: 8 residues processed: 329 average time/residue: 0.1263 time to fit residues: 61.2967 Evaluate side-chains 305 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 295 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain I residue 43 TYR Chi-restraints excluded: chain I residue 102 LYS Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 154 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 chunk 142 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN C 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.171981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.105194 restraints weight = 22279.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 79)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108226 restraints weight = 15330.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110171 restraints weight = 12395.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110916 restraints weight = 10939.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111806 restraints weight = 10255.745| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17470 Z= 0.132 Angle : 0.523 8.117 23714 Z= 0.261 Chirality : 0.040 0.192 2738 Planarity : 0.004 0.052 2886 Dihedral : 10.422 73.140 2964 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.34 % Allowed : 11.88 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.18), residues: 2254 helix: 2.18 (0.15), residues: 1328 sheet: -1.36 (0.44), residues: 112 loop : -1.49 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 229 TYR 0.015 0.001 TYR B 816 PHE 0.015 0.001 PHE D 546 TRP 0.010 0.001 TRP B 460 HIS 0.005 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00309 (17462) covalent geometry : angle 0.52226 (23698) SS BOND : bond 0.00258 ( 8) SS BOND : angle 0.95100 ( 16) hydrogen bonds : bond 0.03788 ( 1036) hydrogen bonds : angle 3.73445 ( 3048) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 319 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 485 ILE cc_start: 0.8676 (tp) cc_final: 0.8267 (tp) REVERT: A 498 ILE cc_start: 0.7787 (mt) cc_final: 0.7534 (mt) REVERT: A 629 ILE cc_start: 0.6070 (OUTLIER) cc_final: 0.5784 (mm) REVERT: A 687 ILE cc_start: 0.7496 (mm) cc_final: 0.7234 (tp) REVERT: A 747 LEU cc_start: 0.9052 (mm) cc_final: 0.8824 (mt) REVERT: B 435 HIS cc_start: 0.6772 (m90) cc_final: 0.6517 (m90) REVERT: B 713 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7692 (mm-30) REVERT: G 35 ARG cc_start: 0.7539 (ttp-170) cc_final: 0.7097 (ttp-170) REVERT: I 102 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8575 (tmmt) REVERT: C 629 ILE cc_start: 0.6183 (OUTLIER) cc_final: 0.5881 (mm) REVERT: C 687 ILE cc_start: 0.7486 (mm) cc_final: 0.7171 (tp) REVERT: C 717 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.7122 (ppp) REVERT: J 26 ILE cc_start: 0.8494 (mm) cc_final: 0.8142 (mt) REVERT: D 713 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7634 (mm-30) REVERT: D 714 GLN cc_start: 0.8328 (mm110) cc_final: 0.8067 (mm110) outliers start: 20 outliers final: 9 residues processed: 326 average time/residue: 0.1409 time to fit residues: 67.3454 Evaluate side-chains 306 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 293 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 102 LYS Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 117 optimal weight: 0.0870 chunk 50 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN C 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.170280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.108487 restraints weight = 22128.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.107328 restraints weight = 15826.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.106508 restraints weight = 13733.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.106608 restraints weight = 13081.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.106734 restraints weight = 12510.287| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17470 Z= 0.146 Angle : 0.514 7.952 23714 Z= 0.259 Chirality : 0.040 0.202 2738 Planarity : 0.003 0.043 2886 Dihedral : 9.838 57.819 2964 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.28 % Allowed : 13.29 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.18), residues: 2254 helix: 2.13 (0.14), residues: 1330 sheet: -1.04 (0.50), residues: 92 loop : -1.41 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 715 TYR 0.021 0.001 TYR D 405 PHE 0.016 0.001 PHE B 546 TRP 0.008 0.001 TRP B 460 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00347 (17462) covalent geometry : angle 0.51309 (23698) SS BOND : bond 0.00312 ( 8) SS BOND : angle 1.11084 ( 16) hydrogen bonds : bond 0.03806 ( 1036) hydrogen bonds : angle 3.70419 ( 3048) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 304 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 485 ILE cc_start: 0.8807 (tp) cc_final: 0.8334 (tp) REVERT: A 498 ILE cc_start: 0.7768 (mt) cc_final: 0.7518 (mt) REVERT: A 687 ILE cc_start: 0.7726 (mm) cc_final: 0.7520 (tp) REVERT: B 435 HIS cc_start: 0.6716 (m90) cc_final: 0.6433 (m90) REVERT: B 714 GLN cc_start: 0.8436 (mm110) cc_final: 0.8101 (mm-40) REVERT: G 35 ARG cc_start: 0.7535 (ttp-170) cc_final: 0.7098 (ttp-170) REVERT: I 43 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.6573 (t80) REVERT: I 102 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8534 (tmmt) REVERT: C 711 ARG cc_start: 0.7222 (mmp80) cc_final: 0.6771 (mmp-170) REVERT: J 26 ILE cc_start: 0.8499 (mm) cc_final: 0.8050 (mt) REVERT: J 43 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.6554 (t80) REVERT: D 594 ARG cc_start: 0.7796 (ttp80) cc_final: 0.7531 (ttp80) REVERT: D 714 GLN cc_start: 0.8397 (mm110) cc_final: 0.8134 (mm-40) outliers start: 34 outliers final: 20 residues processed: 320 average time/residue: 0.1453 time to fit residues: 68.4397 Evaluate side-chains 311 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 288 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 43 TYR Chi-restraints excluded: chain I residue 102 LYS Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 43 TYR Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 92 optimal weight: 2.9990 chunk 176 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 chunk 201 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 125 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN B 619 ASN C 710 GLN J 183 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.172148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3248 r_free = 0.3248 target = 0.109351 restraints weight = 22124.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107883 restraints weight = 15944.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107254 restraints weight = 13938.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.107714 restraints weight = 14357.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.107794 restraints weight = 13477.949| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17470 Z= 0.110 Angle : 0.493 8.048 23714 Z= 0.247 Chirality : 0.039 0.275 2738 Planarity : 0.003 0.040 2886 Dihedral : 9.337 59.416 2964 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.89 % Allowed : 13.22 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.18), residues: 2254 helix: 2.26 (0.15), residues: 1334 sheet: -1.03 (0.50), residues: 92 loop : -1.36 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 657 TYR 0.020 0.001 TYR D 405 PHE 0.012 0.001 PHE E 78 TRP 0.008 0.001 TRP B 460 HIS 0.004 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00245 (17462) covalent geometry : angle 0.49289 (23698) SS BOND : bond 0.00163 ( 8) SS BOND : angle 0.85064 ( 16) hydrogen bonds : bond 0.03452 ( 1036) hydrogen bonds : angle 3.58805 ( 3048) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 313 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 498 ILE cc_start: 0.7686 (mt) cc_final: 0.7432 (mt) REVERT: A 629 ILE cc_start: 0.5822 (OUTLIER) cc_final: 0.5585 (mm) REVERT: B 422 GLU cc_start: 0.7510 (tp30) cc_final: 0.7249 (tp30) REVERT: B 435 HIS cc_start: 0.6676 (m90) cc_final: 0.6383 (m90) REVERT: B 713 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7648 (mm-30) REVERT: B 714 GLN cc_start: 0.8438 (mm110) cc_final: 0.8121 (mm-40) REVERT: G 35 ARG cc_start: 0.7521 (ttp-170) cc_final: 0.7093 (ttp-170) REVERT: I 43 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.6386 (t80) REVERT: I 102 LYS cc_start: 0.8821 (tttm) cc_final: 0.8475 (tmmt) REVERT: C 629 ILE cc_start: 0.6304 (OUTLIER) cc_final: 0.6002 (mm) REVERT: C 711 ARG cc_start: 0.7236 (mmp80) cc_final: 0.6757 (mmp-170) REVERT: J 26 ILE cc_start: 0.8486 (mm) cc_final: 0.8034 (mt) REVERT: D 407 MET cc_start: 0.6705 (mmm) cc_final: 0.6224 (mtt) REVERT: D 594 ARG cc_start: 0.7755 (ttp80) cc_final: 0.7442 (ttp80) REVERT: D 714 GLN cc_start: 0.8472 (mm110) cc_final: 0.8206 (mm-40) outliers start: 43 outliers final: 27 residues processed: 335 average time/residue: 0.1306 time to fit residues: 64.5863 Evaluate side-chains 327 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 297 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 43 TYR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 487 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 33 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 220 optimal weight: 0.0040 chunk 75 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 189 optimal weight: 0.7980 chunk 165 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.171531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107580 restraints weight = 22133.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.106174 restraints weight = 16068.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106750 restraints weight = 14027.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106698 restraints weight = 14774.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.106982 restraints weight = 13162.395| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17470 Z= 0.121 Angle : 0.499 8.470 23714 Z= 0.250 Chirality : 0.039 0.268 2738 Planarity : 0.003 0.041 2886 Dihedral : 9.127 59.482 2964 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.95 % Allowed : 14.77 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.18), residues: 2254 helix: 2.25 (0.14), residues: 1334 sheet: -1.41 (0.49), residues: 104 loop : -1.39 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 657 TYR 0.019 0.001 TYR D 405 PHE 0.012 0.001 PHE E 146 TRP 0.007 0.001 TRP B 460 HIS 0.004 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00278 (17462) covalent geometry : angle 0.49847 (23698) SS BOND : bond 0.00096 ( 8) SS BOND : angle 0.67618 ( 16) hydrogen bonds : bond 0.03489 ( 1036) hydrogen bonds : angle 3.58702 ( 3048) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 309 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 498 ILE cc_start: 0.7741 (mt) cc_final: 0.7480 (mt) REVERT: A 629 ILE cc_start: 0.5848 (OUTLIER) cc_final: 0.5600 (mm) REVERT: A 657 ARG cc_start: 0.8273 (mtm-85) cc_final: 0.7812 (mtm-85) REVERT: B 435 HIS cc_start: 0.6667 (m90) cc_final: 0.6360 (m90) REVERT: B 713 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7462 (mm-30) REVERT: G 35 ARG cc_start: 0.7629 (ttp-170) cc_final: 0.7148 (ttp-170) REVERT: I 43 TYR cc_start: 0.7437 (OUTLIER) cc_final: 0.6469 (t80) REVERT: I 102 LYS cc_start: 0.8798 (tttm) cc_final: 0.8479 (tmmt) REVERT: C 629 ILE cc_start: 0.6265 (OUTLIER) cc_final: 0.5974 (mm) REVERT: C 710 GLN cc_start: 0.6491 (OUTLIER) cc_final: 0.6288 (tt0) REVERT: C 711 ARG cc_start: 0.7225 (mmp80) cc_final: 0.6779 (mmp-170) REVERT: J 26 ILE cc_start: 0.8488 (mm) cc_final: 0.8034 (mt) REVERT: J 43 TYR cc_start: 0.7410 (OUTLIER) cc_final: 0.6308 (t80) REVERT: D 407 MET cc_start: 0.6685 (mmm) cc_final: 0.6199 (mtt) outliers start: 44 outliers final: 31 residues processed: 328 average time/residue: 0.1516 time to fit residues: 72.5743 Evaluate side-chains 325 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 289 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 43 TYR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 710 GLN Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 43 TYR Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 31 optimal weight: 8.9990 chunk 176 optimal weight: 0.6980 chunk 172 optimal weight: 9.9990 chunk 157 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 57 optimal weight: 0.0770 chunk 11 optimal weight: 0.8980 chunk 220 optimal weight: 0.1980 chunk 199 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 183 ASN C 710 GLN J 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.171939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3310 r_free = 0.3310 target = 0.111512 restraints weight = 21988.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.110813 restraints weight = 22883.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112404 restraints weight = 18942.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112534 restraints weight = 16882.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112590 restraints weight = 16288.750| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17470 Z= 0.112 Angle : 0.500 9.510 23714 Z= 0.249 Chirality : 0.039 0.276 2738 Planarity : 0.003 0.041 2886 Dihedral : 8.902 59.945 2964 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.68 % Allowed : 15.70 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.18), residues: 2254 helix: 2.32 (0.14), residues: 1334 sheet: -2.01 (0.42), residues: 148 loop : -1.23 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 657 TYR 0.018 0.001 TYR B 405 PHE 0.013 0.001 PHE E 78 TRP 0.007 0.001 TRP B 460 HIS 0.004 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00253 (17462) covalent geometry : angle 0.49965 (23698) SS BOND : bond 0.00078 ( 8) SS BOND : angle 0.67212 ( 16) hydrogen bonds : bond 0.03380 ( 1036) hydrogen bonds : angle 3.53640 ( 3048) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 300 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 498 ILE cc_start: 0.7930 (mt) cc_final: 0.7665 (mt) REVERT: A 629 ILE cc_start: 0.5374 (OUTLIER) cc_final: 0.5119 (mm) REVERT: B 435 HIS cc_start: 0.6835 (m90) cc_final: 0.6576 (m90) REVERT: G 35 ARG cc_start: 0.7801 (ttp-170) cc_final: 0.7271 (ttp-170) REVERT: I 102 LYS cc_start: 0.8754 (tttm) cc_final: 0.8499 (tmmt) REVERT: I 138 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8510 (mp) REVERT: C 629 ILE cc_start: 0.5985 (OUTLIER) cc_final: 0.5683 (mm) REVERT: C 711 ARG cc_start: 0.7099 (mmp80) cc_final: 0.6799 (mmp-170) REVERT: J 26 ILE cc_start: 0.8515 (mm) cc_final: 0.8068 (mt) REVERT: J 43 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6404 (t80) REVERT: D 407 MET cc_start: 0.6246 (mmm) cc_final: 0.5976 (mtt) REVERT: D 693 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8268 (p) outliers start: 40 outliers final: 32 residues processed: 319 average time/residue: 0.1539 time to fit residues: 71.8331 Evaluate side-chains 323 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 286 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 43 TYR Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 188 optimal weight: 8.9990 chunk 134 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 82 optimal weight: 0.0970 chunk 193 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 183 ASN C 710 GLN J 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.171910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3237 r_free = 0.3237 target = 0.108673 restraints weight = 22133.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.108230 restraints weight = 15087.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107910 restraints weight = 12994.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.108058 restraints weight = 13353.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.108130 restraints weight = 12801.352| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17470 Z= 0.116 Angle : 0.508 11.427 23714 Z= 0.252 Chirality : 0.039 0.255 2738 Planarity : 0.003 0.041 2886 Dihedral : 8.827 59.892 2964 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.02 % Allowed : 16.11 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.18), residues: 2254 helix: 2.34 (0.14), residues: 1330 sheet: -1.81 (0.41), residues: 158 loop : -1.09 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 656 TYR 0.017 0.001 TYR B 405 PHE 0.012 0.001 PHE E 146 TRP 0.007 0.001 TRP B 460 HIS 0.004 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00264 (17462) covalent geometry : angle 0.50751 (23698) SS BOND : bond 0.00082 ( 8) SS BOND : angle 0.67908 ( 16) hydrogen bonds : bond 0.03396 ( 1036) hydrogen bonds : angle 3.53470 ( 3048) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 299 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 498 ILE cc_start: 0.7777 (mt) cc_final: 0.7534 (mt) REVERT: A 629 ILE cc_start: 0.5648 (OUTLIER) cc_final: 0.5415 (mm) REVERT: B 435 HIS cc_start: 0.6722 (m90) cc_final: 0.6430 (m90) REVERT: G 35 ARG cc_start: 0.7635 (ttp-170) cc_final: 0.7146 (ttp-170) REVERT: I 43 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.6391 (t80) REVERT: I 102 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8486 (tmmt) REVERT: I 138 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8477 (mp) REVERT: I 183 ASN cc_start: 0.7916 (OUTLIER) cc_final: 0.7650 (t0) REVERT: C 629 ILE cc_start: 0.6173 (OUTLIER) cc_final: 0.5899 (mm) REVERT: C 711 ARG cc_start: 0.7039 (mmp80) cc_final: 0.6619 (mmp-170) REVERT: J 26 ILE cc_start: 0.8517 (mm) cc_final: 0.8067 (mt) REVERT: J 43 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.6352 (t80) REVERT: D 407 MET cc_start: 0.6677 (mmm) cc_final: 0.6192 (mtt) REVERT: D 460 TRP cc_start: 0.8225 (m100) cc_final: 0.7888 (m100) outliers start: 45 outliers final: 33 residues processed: 321 average time/residue: 0.1530 time to fit residues: 71.9733 Evaluate side-chains 336 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 296 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 43 TYR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 102 LYS Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 43 TYR Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 65 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 202 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 192 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 185 optimal weight: 20.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 107 HIS I 183 ASN C 710 GLN E 101 HIS ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 ASN ** D 709 ASN ** 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 = 0.3972 r_free = 0.3972 target = 0.168712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.148029 restraints weight = 22185.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.146468 restraints weight = 38243.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.144504 restraints weight = 35011.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.143000 restraints weight = 40091.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141144 restraints weight = 38856.643| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 17470 Z= 0.315 Angle : 0.659 10.390 23714 Z= 0.334 Chirality : 0.046 0.264 2738 Planarity : 0.004 0.051 2886 Dihedral : 9.965 59.870 2964 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.89 % Allowed : 16.91 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.18), residues: 2254 helix: 1.68 (0.14), residues: 1342 sheet: -1.82 (0.43), residues: 152 loop : -1.39 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 657 TYR 0.027 0.002 TYR D 405 PHE 0.019 0.002 PHE E 78 TRP 0.015 0.002 TRP I 44 HIS 0.004 0.001 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00775 (17462) covalent geometry : angle 0.65875 (23698) SS BOND : bond 0.00246 ( 8) SS BOND : angle 0.70603 ( 16) hydrogen bonds : bond 0.04732 ( 1036) hydrogen bonds : angle 3.95442 ( 3048) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 289 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 498 ILE cc_start: 0.7902 (mt) cc_final: 0.7684 (mt) REVERT: G 31 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.7045 (m-10) REVERT: C 629 ILE cc_start: 0.5165 (OUTLIER) cc_final: 0.4791 (mm) REVERT: J 26 ILE cc_start: 0.8779 (mm) cc_final: 0.8331 (mt) outliers start: 43 outliers final: 31 residues processed: 313 average time/residue: 0.1535 time to fit residues: 70.6537 Evaluate side-chains 312 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 279 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 51 optimal weight: 0.9990 chunk 221 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 147 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 GLN E 101 HIS J 183 ASN D 619 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.169581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.100414 restraints weight = 22127.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.102410 restraints weight = 17126.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.102704 restraints weight = 14130.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.103066 restraints weight = 13401.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.103688 restraints weight = 12579.396| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17470 Z= 0.135 Angle : 0.541 10.638 23714 Z= 0.269 Chirality : 0.040 0.282 2738 Planarity : 0.003 0.045 2886 Dihedral : 9.279 58.674 2964 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.15 % Allowed : 17.79 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.18), residues: 2254 helix: 1.99 (0.14), residues: 1344 sheet: -1.47 (0.45), residues: 146 loop : -1.20 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 656 TYR 0.020 0.001 TYR D 405 PHE 0.011 0.001 PHE E 146 TRP 0.019 0.001 TRP D 460 HIS 0.005 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00315 (17462) covalent geometry : angle 0.54034 (23698) SS BOND : bond 0.00050 ( 8) SS BOND : angle 0.76333 ( 16) hydrogen bonds : bond 0.03684 ( 1036) hydrogen bonds : angle 3.65912 ( 3048) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 295 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 498 ILE cc_start: 0.7790 (mt) cc_final: 0.7540 (mt) REVERT: A 657 ARG cc_start: 0.7941 (mtt90) cc_final: 0.7598 (mtm-85) REVERT: G 31 PHE cc_start: 0.6978 (OUTLIER) cc_final: 0.6481 (m-10) REVERT: G 35 ARG cc_start: 0.7561 (ttp-170) cc_final: 0.7259 (ttp-170) REVERT: I 138 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8395 (mp) REVERT: J 26 ILE cc_start: 0.8359 (mm) cc_final: 0.7905 (mt) REVERT: D 693 VAL cc_start: 0.8394 (OUTLIER) cc_final: 0.8151 (p) outliers start: 32 outliers final: 23 residues processed: 314 average time/residue: 0.1544 time to fit residues: 71.0651 Evaluate side-chains 317 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 291 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 17 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 209 optimal weight: 0.4980 chunk 192 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.169864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.101878 restraints weight = 22236.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.103848 restraints weight = 16365.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.104185 restraints weight = 12336.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.104287 restraints weight = 11992.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.104488 restraints weight = 11497.504| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17470 Z= 0.129 Angle : 0.536 10.461 23714 Z= 0.266 Chirality : 0.040 0.284 2738 Planarity : 0.003 0.041 2886 Dihedral : 8.874 58.977 2964 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.95 % Allowed : 18.39 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.18), residues: 2254 helix: 2.11 (0.14), residues: 1344 sheet: -1.58 (0.41), residues: 172 loop : -1.04 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 657 TYR 0.017 0.001 TYR D 405 PHE 0.019 0.001 PHE E 78 TRP 0.016 0.001 TRP D 460 HIS 0.003 0.001 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00300 (17462) covalent geometry : angle 0.53620 (23698) SS BOND : bond 0.00093 ( 8) SS BOND : angle 0.80485 ( 16) hydrogen bonds : bond 0.03608 ( 1036) hydrogen bonds : angle 3.60217 ( 3048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3133.48 seconds wall clock time: 55 minutes 0.36 seconds (3300.36 seconds total)