Starting phenix.real_space_refine on Sun Aug 24 02:39:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5vot_8721/08_2025/5vot_8721_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vot_8721/08_2025/5vot_8721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5vot_8721/08_2025/5vot_8721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vot_8721/08_2025/5vot_8721.map" model { file = "/net/cci-nas-00/data/ceres_data/5vot_8721/08_2025/5vot_8721_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vot_8721/08_2025/5vot_8721_neut.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 95 5.16 5 C 10662 2.51 5 N 2666 2.21 5 O 3040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s 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: 16463 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3049 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 30} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 395} Chain breaks: 2 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3046 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 31} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 395} Chain breaks: 2 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 70 Chain: "D" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3028 Classifications: {'peptide': 409} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 38} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 396} Chain breaks: 2 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 7, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 92 Chain: "E" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1007 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 4 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 282 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ARG:plan': 9, 'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 3, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 177 Chain: "F" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1149 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 9, 'GLN:plan1': 3, 'ASP:plan': 4, 'TYR:plan': 2, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 152 Chain: "G" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1007 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 4 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 282 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ARG:plan': 9, 'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 3, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 177 Chain: "H" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1149 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 9, 'GLN:plan1': 3, 'ASP:plan': 4, 'TYR:plan': 2, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 152 Chain: "B" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3028 Classifications: {'peptide': 409} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 38} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 396} Chain breaks: 2 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 7, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 92 Time building chain proxies: 3.51, per 1000 atoms: 0.21 Number of scatterers: 16463 At special positions: 0 Unit cell: (125.56, 115.24, 147.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 95 16.00 O 3040 8.00 N 2666 7.00 C 10662 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 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: 1.57 Conformation dependent library (CDL) restraints added in 617.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 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: 90 helices and 24 sheets defined 59.6% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 522 through 546 removed outlier: 3.521A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 571 removed outlier: 3.504A pdb=" N PHE A 571 " --> pdb=" O THR A 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 568 through 571' Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 625 removed outlier: 4.517A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 641 removed outlier: 3.600A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 675 Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 757 Processing helix chain 'A' and resid 757 through 767 removed outlier: 3.663A pdb=" N LYS A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 825 removed outlier: 4.170A pdb=" N ALA A 793 " --> pdb=" O LEU A 789 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE A 798 " --> pdb=" O GLY A 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 513 through 517 Processing helix chain 'C' and resid 522 through 546 removed outlier: 3.523A pdb=" N TRP C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 571 removed outlier: 3.501A pdb=" N PHE C 571 " --> pdb=" O THR C 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 568 through 571' Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 625 removed outlier: 4.493A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 641 removed outlier: 3.600A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 675 Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 767 removed outlier: 3.689A pdb=" N LYS C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 825 removed outlier: 5.476A pdb=" N ILE C 798 " --> pdb=" O GLY C 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 512 through 518 removed outlier: 4.273A pdb=" N PHE D 515 " --> pdb=" O PRO D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 545 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 597 through 621 removed outlier: 3.787A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA D 621 " --> pdb=" O THR D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 removed outlier: 3.593A pdb=" N LYS D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.923A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 757 Processing helix chain 'D' and resid 757 through 768 removed outlier: 3.585A pdb=" N LYS D 761 " --> pdb=" O GLY D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 824 removed outlier: 3.725A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY D 801 " --> pdb=" O TYR D 797 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY D 804 " --> pdb=" O VAL D 800 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA D 810 " --> pdb=" O ALA D 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 30 Processing helix chain 'E' and resid 93 through 103 Processing helix chain 'E' and resid 105 through 127 removed outlier: 3.661A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 160 removed outlier: 3.554A pdb=" N SER E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 212 removed outlier: 3.901A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 30 removed outlier: 3.518A pdb=" N THR F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 103 Processing helix chain 'F' and resid 105 through 127 removed outlier: 4.568A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 160 removed outlier: 3.861A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 213 removed outlier: 3.645A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG F 213 " --> pdb=" O ARG F 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 30 Processing helix chain 'G' and resid 93 through 103 Processing helix chain 'G' and resid 105 through 127 removed outlier: 3.664A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 160 removed outlier: 3.533A pdb=" N SER G 137 " --> pdb=" O ASN G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 211 removed outlier: 3.899A pdb=" N TYR G 181 " --> pdb=" O GLY G 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 30 removed outlier: 3.523A pdb=" N THR H 30 " --> pdb=" O ILE H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 103 Processing helix chain 'H' and resid 105 through 127 removed outlier: 4.570A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 160 removed outlier: 3.870A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 213 removed outlier: 3.636A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG H 213 " --> pdb=" O ARG H 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 512 through 518 removed outlier: 4.271A pdb=" N PHE B 515 " --> pdb=" O PRO B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 545 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 597 through 621 removed outlier: 3.787A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA B 621 " --> pdb=" O THR B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 641 removed outlier: 3.592A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.922A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 757 Processing helix chain 'B' and resid 757 through 768 removed outlier: 3.581A pdb=" N LYS B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 824 removed outlier: 3.724A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLY B 801 " --> pdb=" O TYR B 797 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 804 " --> pdb=" O VAL B 800 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA B 810 " --> pdb=" O ALA B 806 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 439 through 444 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 490 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.655A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.294A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 439 through 444 Processing sheet with id=AA7, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AA9, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.653A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.297A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 440 through 444 Processing sheet with id=AB3, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AB5, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.884A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.234A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 33 through 36 Processing sheet with id=AB8, first strand: chain 'F' and resid 33 through 36 Processing sheet with id=AB9, first strand: chain 'G' and resid 33 through 35 Processing sheet with id=AC1, first strand: chain 'H' and resid 33 through 36 Processing sheet with id=AC2, first strand: chain 'B' and resid 440 through 444 Processing sheet with id=AC3, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AC4, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AC5, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.879A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.247A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) 1098 hydrogen bonds defined for protein. 3165 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: 2.65 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5185 1.34 - 1.46: 4239 1.46 - 1.58: 7217 1.58 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 16791 Sorted by residual: bond pdb=" C GLY A 588 " pdb=" N CYS A 589 " ideal model delta sigma weight residual 1.330 1.535 -0.206 1.37e-02 5.33e+03 2.26e+02 bond pdb=" N GLN A 587 " pdb=" CA GLN A 587 " ideal model delta sigma weight residual 1.457 1.432 0.025 1.29e-02 6.01e+03 3.86e+00 bond pdb=" CA GLN A 587 " pdb=" C GLN A 587 " ideal model delta sigma weight residual 1.523 1.502 0.022 1.34e-02 5.57e+03 2.61e+00 bond pdb=" C LYS B 505 " pdb=" N LYS B 506 " ideal model delta sigma weight residual 1.331 1.369 -0.038 3.12e-02 1.03e+03 1.47e+00 bond pdb=" C LYS D 505 " pdb=" N LYS D 506 " ideal model delta sigma weight residual 1.331 1.368 -0.037 3.12e-02 1.03e+03 1.39e+00 ... (remaining 16786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 22749 3.61 - 7.22: 77 7.22 - 10.83: 6 10.83 - 14.44: 2 14.44 - 18.04: 3 Bond angle restraints: 22837 Sorted by residual: angle pdb=" CA GLY A 588 " pdb=" C GLY A 588 " pdb=" N CYS A 589 " ideal model delta sigma weight residual 114.96 96.92 18.04 1.15e+00 7.56e-01 2.46e+02 angle pdb=" O GLY A 588 " pdb=" C GLY A 588 " pdb=" N CYS A 589 " ideal model delta sigma weight residual 123.02 139.27 -16.25 1.98e+00 2.55e-01 6.73e+01 angle pdb=" C GLY A 588 " pdb=" N CYS A 589 " pdb=" CA CYS A 589 " ideal model delta sigma weight residual 121.32 104.45 16.87 2.10e+00 2.27e-01 6.45e+01 angle pdb=" N VAL C 795 " pdb=" CA VAL C 795 " pdb=" C VAL C 795 " ideal model delta sigma weight residual 113.53 108.09 5.44 9.80e-01 1.04e+00 3.08e+01 angle pdb=" N GLY C 423 " pdb=" CA GLY C 423 " pdb=" C GLY C 423 " ideal model delta sigma weight residual 110.56 115.27 -4.71 1.36e+00 5.41e-01 1.20e+01 ... (remaining 22832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.90: 8810 8.90 - 17.79: 669 17.79 - 26.69: 117 26.69 - 35.59: 79 35.59 - 44.48: 10 Dihedral angle restraints: 9685 sinusoidal: 3069 harmonic: 6616 Sorted by residual: dihedral pdb=" CA ALA B 522 " pdb=" C ALA B 522 " pdb=" N TYR B 523 " pdb=" CA TYR B 523 " ideal model delta harmonic sigma weight residual 180.00 151.79 28.21 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA ALA D 522 " pdb=" C ALA D 522 " pdb=" N TYR D 523 " pdb=" CA TYR D 523 " ideal model delta harmonic sigma weight residual 180.00 152.56 27.44 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA PHE D 796 " pdb=" C PHE D 796 " pdb=" N TYR D 797 " pdb=" CA TYR D 797 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 9682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1834 0.033 - 0.066: 615 0.066 - 0.100: 179 0.100 - 0.133: 49 0.133 - 0.166: 3 Chirality restraints: 2680 Sorted by residual: chirality pdb=" CA PRO C 520 " pdb=" N PRO C 520 " pdb=" C PRO C 520 " pdb=" CB PRO C 520 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CA PRO A 520 " pdb=" N PRO A 520 " pdb=" C PRO A 520 " pdb=" CB PRO A 520 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA TYR B 797 " pdb=" N TYR B 797 " pdb=" C TYR B 797 " pdb=" CB TYR B 797 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 2677 not shown) Planarity restraints: 2866 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 588 " 0.015 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C GLY A 588 " -0.064 2.00e-02 2.50e+03 pdb=" O GLY A 588 " 0.029 2.00e-02 2.50e+03 pdb=" N CYS A 589 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 606 " 0.016 2.00e-02 2.50e+03 1.49e-02 5.52e+00 pdb=" CG TRP A 606 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 606 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 606 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 606 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 606 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 606 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 606 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 606 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 606 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 606 " -0.016 2.00e-02 2.50e+03 1.45e-02 5.23e+00 pdb=" CG TRP C 606 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C 606 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 606 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 606 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 606 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 606 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 606 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 606 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 606 " -0.002 2.00e-02 2.50e+03 ... (remaining 2863 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 357 2.68 - 3.24: 18212 3.24 - 3.79: 25129 3.79 - 4.35: 32939 4.35 - 4.90: 50779 Nonbonded interactions: 127416 Sorted by model distance: nonbonded pdb=" O PRO F 108 " pdb=" OG SER F 111 " model vdw 2.126 3.040 nonbonded pdb=" O PRO H 108 " pdb=" OG SER H 111 " model vdw 2.126 3.040 nonbonded pdb=" O GLN F 9 " pdb=" OG1 THR F 13 " model vdw 2.143 3.040 nonbonded pdb=" OE1 GLU A 705 " pdb=" OH TYR A 732 " model vdw 2.144 3.040 nonbonded pdb=" O GLN H 9 " pdb=" OG1 THR H 13 " model vdw 2.145 3.040 ... (remaining 127411 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 391 through 509 or (resid 510 through 511 and (name N or n \ ame CA or name C or name O or name CB )) or resid 512 through 518 or (resid 519 \ and (name N or name CA or name C or name O or name CB )) or resid 520 through 52 \ 4 or (resid 525 and (name N or name CA or name C or name O or name CB )) or resi \ d 526 or (resid 527 and (name N or name CA or name C or name O or name CB )) or \ resid 528 through 545 or (resid 546 and (name N or name CA or name C or name O o \ r name CB )) or resid 547 through 568 or (resid 569 through 571 and (name N or n \ ame CA or name C or name O or name CB )) or resid 572 through 584 or (resid 585 \ and (name N or name CA or name C or name O or name CB )) or resid 586 through 62 \ 4 or (resid 625 through 630 and (name N or name CA or name C or name O or name C \ B )) or resid 631 through 788 or (resid 789 and (name N or name CA or name C or \ name O or name CB )) or resid 790 through 806 or (resid 807 and (name N or name \ CA or name C or name O or name CB )) or resid 808 through 820 or (resid 821 thro \ ugh 825 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 391 through 504 or (resid 505 through 506 and (name N or n \ ame CA or name C or name O or name CB )) or resid 507 through 566 or (resid 567 \ and (name N or name CA or name C or name O or name CB )) or resid 568 through 58 \ 6 or (resid 587 and (name N or name CA or name C or name O or name CB )) or resi \ d 588 through 632 or (resid 633 through 634 and (name N or name CA or name C or \ name O or name CB )) or resid 635 through 774 or resid 785 through 786 or (resid \ 787 and (name N or name CA or name C or name O or name CB )) or resid 788 throu \ gh 825)) selection = (chain 'C' and (resid 391 through 509 or (resid 510 through 511 and (name N or n \ ame CA or name C or name O or name CB )) or resid 512 through 518 or (resid 519 \ and (name N or name CA or name C or name O or name CB )) or resid 520 through 52 \ 4 or (resid 525 and (name N or name CA or name C or name O or name CB )) or resi \ d 526 or (resid 527 and (name N or name CA or name C or name O or name CB )) or \ resid 528 through 545 or (resid 546 and (name N or name CA or name C or name O o \ r name CB )) or resid 547 through 568 or (resid 569 through 571 and (name N or n \ ame CA or name C or name O or name CB )) or resid 572 through 584 or (resid 585 \ and (name N or name CA or name C or name O or name CB )) or resid 586 through 62 \ 4 or (resid 625 through 630 and (name N or name CA or name C or name O or name C \ B )) or resid 631 through 788 or (resid 789 and (name N or name CA or name C or \ name O or name CB )) or resid 790 through 806 or (resid 807 and (name N or name \ CA or name C or name O or name CB )) or resid 808 through 820 or (resid 821 thro \ ugh 825 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 391 through 504 or (resid 505 through 506 and (name N or n \ ame CA or name C or name O or name CB )) or resid 507 through 566 or (resid 567 \ and (name N or name CA or name C or name O or name CB )) or resid 568 through 58 \ 6 or (resid 587 and (name N or name CA or name C or name O or name CB )) or resi \ d 588 through 632 or (resid 633 through 634 and (name N or name CA or name C or \ name O or name CB )) or resid 635 through 774 or resid 785 through 786 or (resid \ 787 and (name N or name CA or name C or name O or name CB )) or resid 788 throu \ gh 825)) } ncs_group { reference = (chain 'E' and (resid 6 through 22 or (resid 23 through 24 and (name N or name C \ A or name C or name O or name CB )) or resid 25 through 100 or (resid 101 throug \ h 105 and (name N or name CA or name C or name O or name CB )) or resid 106 thro \ ugh 148 or (resid 149 through 151 and (name N or name CA or name C or name O or \ name CB )) or (resid 152 through 155 and (name N or name CA or name C or name O \ or name CB )) or resid 156 through 185 or (resid 186 through 187 and (name N or \ name CA or name C or name O or name CB )) or resid 188 through 199 or (resid 200 \ through 201 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 02 through 213)) selection = (chain 'F' and ((resid 6 through 12 and (name N or name CA or name C or name O o \ r name CB )) or resid 13 or (resid 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 25 or (resid 26 through 27 and (name N or nam \ e CA or name C or name O or name CB )) or resid 28 through 29 or (resid 30 throu \ gh 33 and (name N or name CA or name C or name O or name CB )) or resid 34 or (r \ esid 35 through 37 and (name N or name CA or name C or name O or name CB )) or r \ esid 38 or (resid 57 through 61 and (name N or name CA or name C or name O or na \ me CB )) or resid 62 or (resid 63 through 66 and (name N or name CA or name C or \ name O or name CB )) or resid 67 or (resid 68 through 74 and (name N or name CA \ or name C or name O or name CB )) or resid 75 through 85 or (resid 86 and (name \ N or name CA or name C or name O or name CB )) or (resid 93 through 95 and (nam \ e N or name CA or name C or name O or name CB )) or resid 96 through 97 or (resi \ d 98 through 105 and (name N or name CA or name C or name O or name CB )) or res \ id 106 or (resid 107 and (name N or name CA or name C or name O or name CB )) or \ resid 108 through 110 or (resid 111 through 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 or (resid 114 and (name N or name CA or n \ ame C or name O or name CB )) or resid 115 through 116 or (resid 117 and (name N \ or name CA or name C or name O or name CB )) or (resid 118 through 136 and (nam \ e N or name CA or name C or name O or name CB )) or resid 137 through 139 or (re \ sid 140 and (name N or name CA or name C or name O or name CB )) or resid 141 th \ rough 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) \ or resid 148 through 149 or (resid 150 through 151 and (name N or name CA or na \ me C or name O or name CB )) or resid 152 or (resid 153 through 155 and (name N \ or name CA or name C or name O or name CB )) or resid 156 or (resid 157 and (nam \ e N or name CA or name C or name O or name CB )) or resid 158 through 159 or (re \ sid 160 through 161 and (name N or name CA or name C or name O or name CB )) or \ resid 174 through 178 or (resid 179 and (name N or name CA or name C or name O o \ r name CB )) or resid 180 through 190 or (resid 191 through 193 and (name N or n \ ame CA or name C or name O or name CB )) or resid 194 through 204 or (resid 205 \ through 213 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'G' and (resid 6 through 22 or (resid 23 through 24 and (name N or name C \ A or name C or name O or name CB )) or resid 25 through 100 or (resid 101 throug \ h 105 and (name N or name CA or name C or name O or name CB )) or resid 106 thro \ ugh 148 or (resid 149 through 151 and (name N or name CA or name C or name O or \ name CB )) or (resid 152 through 155 and (name N or name CA or name C or name O \ or name CB )) or resid 156 through 185 or (resid 186 through 187 and (name N or \ name CA or name C or name O or name CB )) or resid 188 through 199 or (resid 200 \ through 201 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 02 through 213)) selection = (chain 'H' and ((resid 6 through 12 and (name N or name CA or name C or name O o \ r name CB )) or resid 13 or (resid 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 25 or (resid 26 through 27 and (name N or nam \ e CA or name C or name O or name CB )) or resid 28 through 29 or (resid 30 throu \ gh 33 and (name N or name CA or name C or name O or name CB )) or resid 34 or (r \ esid 35 through 37 and (name N or name CA or name C or name O or name CB )) or r \ esid 38 or (resid 57 through 61 and (name N or name CA or name C or name O or na \ me CB )) or resid 62 or (resid 63 through 66 and (name N or name CA or name C or \ name O or name CB )) or resid 67 or (resid 68 through 74 and (name N or name CA \ or name C or name O or name CB )) or resid 75 through 85 or (resid 86 and (name \ N or name CA or name C or name O or name CB )) or (resid 93 through 95 and (nam \ e N or name CA or name C or name O or name CB )) or resid 96 through 97 or (resi \ d 98 through 105 and (name N or name CA or name C or name O or name CB )) or res \ id 106 or (resid 107 and (name N or name CA or name C or name O or name CB )) or \ resid 108 through 110 or (resid 111 through 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 or (resid 114 and (name N or name CA or n \ ame C or name O or name CB )) or resid 115 through 116 or (resid 117 and (name N \ or name CA or name C or name O or name CB )) or (resid 118 through 136 and (nam \ e N or name CA or name C or name O or name CB )) or resid 137 through 139 or (re \ sid 140 and (name N or name CA or name C or name O or name CB )) or resid 141 th \ rough 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) \ or resid 148 through 149 or (resid 150 through 151 and (name N or name CA or na \ me C or name O or name CB )) or resid 152 or (resid 153 through 155 and (name N \ or name CA or name C or name O or name CB )) or resid 156 or (resid 157 and (nam \ e N or name CA or name C or name O or name CB )) or resid 158 through 159 or (re \ sid 160 through 161 and (name N or name CA or name C or name O or name CB )) or \ resid 174 through 178 or (resid 179 and (name N or name CA or name C or name O o \ r name CB )) or resid 180 through 190 or (resid 191 through 193 and (name N or n \ ame CA or name C or name O or name CB )) or resid 194 through 204 or (resid 205 \ through 213 and (name N or name CA or name C or name O or name CB )))) } 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: 0.850 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.160 Find NCS groups from input model: 0.310 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: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 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 : 0.004 0.206 16799 Z= 0.214 Angle : 0.666 18.045 22853 Z= 0.384 Chirality : 0.038 0.166 2680 Planarity : 0.004 0.048 2866 Dihedral : 7.574 44.482 5433 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: -4.03 (0.14), residues: 2262 helix: -2.21 (0.11), residues: 1280 sheet: -2.83 (0.38), residues: 140 loop : -3.22 (0.18), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 715 TYR 0.018 0.002 TYR B 797 PHE 0.015 0.002 PHE D 814 TRP 0.038 0.003 TRP A 606 HIS 0.004 0.001 HIS F 199 Details of bonding type rmsd covalent geometry : bond 0.00390 (16791) covalent geometry : angle 0.66593 (22837) SS BOND : bond 0.00280 ( 8) SS BOND : angle 0.42333 ( 16) hydrogen bonds : bond 0.13347 ( 1098) hydrogen bonds : angle 9.87728 ( 3165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 548 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 TYR cc_start: 0.8281 (t80) cc_final: 0.8025 (t80) REVERT: A 527 MET cc_start: 0.8195 (mtm) cc_final: 0.7739 (mtp) REVERT: A 608 PHE cc_start: 0.8715 (t80) cc_final: 0.8412 (t80) REVERT: C 424 TYR cc_start: 0.8314 (t80) cc_final: 0.8029 (t80) REVERT: C 527 MET cc_start: 0.8164 (mtm) cc_final: 0.7771 (mtp) REVERT: C 608 PHE cc_start: 0.8718 (t80) cc_final: 0.8415 (t80) REVERT: C 659 PHE cc_start: 0.7367 (m-80) cc_final: 0.7160 (m-10) REVERT: C 703 LEU cc_start: 0.8685 (mt) cc_final: 0.8279 (mt) REVERT: D 405 TYR cc_start: 0.7775 (m-80) cc_final: 0.7303 (m-80) REVERT: D 425 CYS cc_start: 0.8765 (m) cc_final: 0.8172 (m) REVERT: D 483 LEU cc_start: 0.9119 (tp) cc_final: 0.8454 (tp) REVERT: D 498 LEU cc_start: 0.9405 (pp) cc_final: 0.9152 (pp) REVERT: D 503 MET cc_start: 0.7778 (ttm) cc_final: 0.7050 (ttm) REVERT: D 606 TRP cc_start: 0.8741 (m-10) cc_final: 0.8433 (m-10) REVERT: D 674 MET cc_start: 0.8148 (mtm) cc_final: 0.7912 (ptp) REVERT: D 750 VAL cc_start: 0.9237 (t) cc_final: 0.8972 (t) REVERT: E 155 VAL cc_start: 0.6311 (t) cc_final: 0.6053 (t) REVERT: F 141 PHE cc_start: -0.1535 (m-10) cc_final: -0.1851 (m-10) REVERT: F 151 ILE cc_start: 0.6200 (mt) cc_final: 0.5733 (mt) REVERT: F 195 VAL cc_start: 0.8985 (t) cc_final: 0.8768 (t) REVERT: G 195 VAL cc_start: 0.9027 (t) cc_final: 0.8808 (t) REVERT: H 136 LEU cc_start: 0.6389 (mt) cc_final: 0.6159 (mp) REVERT: H 141 PHE cc_start: -0.1533 (m-10) cc_final: -0.1853 (m-10) REVERT: H 151 ILE cc_start: 0.6209 (mt) cc_final: 0.5674 (mt) REVERT: B 405 TYR cc_start: 0.7789 (m-80) cc_final: 0.7485 (m-80) REVERT: B 425 CYS cc_start: 0.8579 (m) cc_final: 0.8235 (m) REVERT: B 483 LEU cc_start: 0.9105 (tp) cc_final: 0.8524 (tp) REVERT: B 498 LEU cc_start: 0.9397 (pp) cc_final: 0.9133 (pp) REVERT: B 503 MET cc_start: 0.7479 (ttm) cc_final: 0.6821 (ttm) REVERT: B 606 TRP cc_start: 0.8708 (m-10) cc_final: 0.8434 (m-10) REVERT: B 750 VAL cc_start: 0.9227 (t) cc_final: 0.8981 (t) outliers start: 0 outliers final: 0 residues processed: 548 average time/residue: 0.1117 time to fit residues: 92.1260 Evaluate side-chains 344 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.0370 chunk 103 optimal weight: 0.2980 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 overall best weight: 2.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN D 764 ASN F 199 HIS H 199 HIS ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN B 764 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.069320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.056145 restraints weight = 77695.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.057536 restraints weight = 54905.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.058465 restraints weight = 41726.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.059195 restraints weight = 34130.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.059737 restraints weight = 28919.792| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16799 Z= 0.202 Angle : 0.660 12.073 22853 Z= 0.350 Chirality : 0.042 0.193 2680 Planarity : 0.004 0.046 2866 Dihedral : 4.644 28.036 2428 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.27 % Allowed : 3.09 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: -1.51 (0.17), residues: 2262 helix: 0.27 (0.14), residues: 1306 sheet: -2.30 (0.37), residues: 170 loop : -2.90 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 586 TYR 0.024 0.002 TYR B 797 PHE 0.043 0.002 PHE B 814 TRP 0.027 0.002 TRP C 606 HIS 0.004 0.001 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.00416 (16791) covalent geometry : angle 0.65604 (22837) SS BOND : bond 0.00411 ( 8) SS BOND : angle 2.81201 ( 16) hydrogen bonds : bond 0.04202 ( 1098) hydrogen bonds : angle 5.50678 ( 3165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 445 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 TYR cc_start: 0.9598 (t80) cc_final: 0.9052 (t80) REVERT: A 463 MET cc_start: 0.9025 (mtm) cc_final: 0.8015 (mpp) REVERT: A 498 LEU cc_start: 0.9236 (pp) cc_final: 0.8454 (pp) REVERT: A 527 MET cc_start: 0.8832 (mtm) cc_final: 0.7873 (mtp) REVERT: A 528 CYS cc_start: 0.9243 (m) cc_final: 0.8981 (m) REVERT: A 660 ARG cc_start: 0.8846 (ptm160) cc_final: 0.8618 (ptp-110) REVERT: A 726 ASN cc_start: 0.8997 (m-40) cc_final: 0.8552 (t0) REVERT: A 760 ASP cc_start: 0.9102 (p0) cc_final: 0.8885 (t0) REVERT: A 799 LEU cc_start: 0.9238 (tp) cc_final: 0.8929 (tp) REVERT: C 424 TYR cc_start: 0.9621 (t80) cc_final: 0.9090 (t80) REVERT: C 463 MET cc_start: 0.8571 (mpp) cc_final: 0.8123 (mpp) REVERT: C 498 LEU cc_start: 0.9163 (pp) cc_final: 0.8509 (pp) REVERT: C 527 MET cc_start: 0.8808 (mtm) cc_final: 0.7828 (mtp) REVERT: C 528 CYS cc_start: 0.9242 (m) cc_final: 0.8987 (m) REVERT: C 660 ARG cc_start: 0.8890 (ptm160) cc_final: 0.8477 (ptp-110) REVERT: C 726 ASN cc_start: 0.9013 (m-40) cc_final: 0.8764 (t0) REVERT: C 760 ASP cc_start: 0.9111 (p0) cc_final: 0.8891 (t0) REVERT: C 799 LEU cc_start: 0.9240 (tp) cc_final: 0.8937 (tp) REVERT: D 399 THR cc_start: 0.8568 (t) cc_final: 0.8204 (m) REVERT: D 405 TYR cc_start: 0.8558 (m-80) cc_final: 0.8006 (m-80) REVERT: D 503 MET cc_start: 0.9057 (ttm) cc_final: 0.8310 (ttm) REVERT: D 613 ILE cc_start: 0.9623 (pt) cc_final: 0.9399 (mp) REVERT: D 756 GLN cc_start: 0.8890 (mt0) cc_final: 0.8611 (mt0) REVERT: E 22 SER cc_start: 0.8996 (t) cc_final: 0.8703 (p) REVERT: E 23 LEU cc_start: 0.9090 (mt) cc_final: 0.8849 (mt) REVERT: E 142 PHE cc_start: 0.9579 (t80) cc_final: 0.9251 (t80) REVERT: F 115 LEU cc_start: 0.9673 (tt) cc_final: 0.9459 (tp) REVERT: F 117 MET cc_start: 0.8861 (tpt) cc_final: 0.8243 (tpt) REVERT: F 121 CYS cc_start: 0.8421 (m) cc_final: 0.8056 (m) REVERT: G 22 SER cc_start: 0.8746 (t) cc_final: 0.8297 (p) REVERT: G 23 LEU cc_start: 0.8554 (mm) cc_final: 0.8132 (mm) REVERT: G 142 PHE cc_start: 0.9607 (t80) cc_final: 0.9290 (t80) REVERT: H 115 LEU cc_start: 0.9663 (tt) cc_final: 0.9447 (tp) REVERT: H 117 MET cc_start: 0.8886 (tpt) cc_final: 0.8265 (tpt) REVERT: H 121 CYS cc_start: 0.8456 (m) cc_final: 0.8094 (m) REVERT: B 399 THR cc_start: 0.8605 (t) cc_final: 0.8200 (m) REVERT: B 402 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8392 (mp0) REVERT: B 405 TYR cc_start: 0.8773 (m-80) cc_final: 0.7738 (m-80) REVERT: B 414 MET cc_start: 0.8576 (mpp) cc_final: 0.8371 (mpp) REVERT: B 463 MET cc_start: 0.8387 (mtt) cc_final: 0.8172 (mtt) REVERT: B 483 LEU cc_start: 0.9475 (tp) cc_final: 0.8998 (mp) REVERT: B 503 MET cc_start: 0.9016 (ttm) cc_final: 0.8212 (ttm) REVERT: B 613 ILE cc_start: 0.9606 (pt) cc_final: 0.9403 (mp) REVERT: B 756 GLN cc_start: 0.8909 (mt0) cc_final: 0.8628 (mt0) outliers start: 4 outliers final: 0 residues processed: 447 average time/residue: 0.0943 time to fit residues: 68.1542 Evaluate side-chains 327 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 51 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 218 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN B 435 HIS ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.066992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.053488 restraints weight = 80501.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.054887 restraints weight = 54972.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.055908 restraints weight = 41216.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.056648 restraints weight = 33059.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.057152 restraints weight = 27792.664| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16799 Z= 0.254 Angle : 0.698 11.604 22853 Z= 0.369 Chirality : 0.043 0.166 2680 Planarity : 0.004 0.044 2866 Dihedral : 4.937 32.159 2428 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.13 % Allowed : 3.76 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.97 (0.17), residues: 2262 helix: 0.75 (0.14), residues: 1304 sheet: -2.20 (0.34), residues: 186 loop : -2.71 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 485 TYR 0.022 0.002 TYR B 523 PHE 0.024 0.002 PHE F 142 TRP 0.016 0.002 TRP B 671 HIS 0.005 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00515 (16791) covalent geometry : angle 0.69729 (22837) SS BOND : bond 0.00563 ( 8) SS BOND : angle 1.67528 ( 16) hydrogen bonds : bond 0.04312 ( 1098) hydrogen bonds : angle 5.26495 ( 3165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 395 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 THR cc_start: 0.8824 (t) cc_final: 0.8402 (t) REVERT: A 424 TYR cc_start: 0.9634 (t80) cc_final: 0.9026 (t80) REVERT: A 463 MET cc_start: 0.8946 (mtm) cc_final: 0.8110 (mpp) REVERT: A 466 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7529 (mt-10) REVERT: A 485 ARG cc_start: 0.9532 (mtt180) cc_final: 0.9124 (mtt180) REVERT: A 503 MET cc_start: 0.7854 (ttm) cc_final: 0.7405 (ttm) REVERT: A 527 MET cc_start: 0.8885 (mtm) cc_final: 0.8207 (mtt) REVERT: A 657 GLU cc_start: 0.9168 (tp30) cc_final: 0.8844 (tp30) REVERT: C 399 THR cc_start: 0.8439 (t) cc_final: 0.8045 (t) REVERT: C 424 TYR cc_start: 0.9644 (t80) cc_final: 0.9087 (t80) REVERT: C 503 MET cc_start: 0.7898 (ttm) cc_final: 0.7434 (ttm) REVERT: C 527 MET cc_start: 0.8858 (mtm) cc_final: 0.8170 (mtt) REVERT: C 657 GLU cc_start: 0.9182 (tp30) cc_final: 0.8870 (tp30) REVERT: D 402 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8520 (mp0) REVERT: D 405 TYR cc_start: 0.8573 (m-80) cc_final: 0.7903 (m-80) REVERT: D 463 MET cc_start: 0.8500 (mtm) cc_final: 0.8166 (ttm) REVERT: D 756 GLN cc_start: 0.8957 (mt0) cc_final: 0.8724 (mt0) REVERT: E 22 SER cc_start: 0.8756 (t) cc_final: 0.8443 (p) REVERT: E 23 LEU cc_start: 0.9070 (mt) cc_final: 0.8835 (mt) REVERT: E 142 PHE cc_start: 0.9543 (t80) cc_final: 0.9202 (t80) REVERT: E 181 TYR cc_start: 0.9151 (m-10) cc_final: 0.8862 (m-80) REVERT: F 114 LEU cc_start: 0.9347 (tp) cc_final: 0.9105 (tp) REVERT: F 117 MET cc_start: 0.8488 (tpt) cc_final: 0.7976 (tpt) REVERT: F 121 CYS cc_start: 0.8585 (m) cc_final: 0.8253 (m) REVERT: G 22 SER cc_start: 0.8553 (t) cc_final: 0.8091 (p) REVERT: G 23 LEU cc_start: 0.8417 (mm) cc_final: 0.7852 (mm) REVERT: G 142 PHE cc_start: 0.9526 (t80) cc_final: 0.9160 (t80) REVERT: G 181 TYR cc_start: 0.9217 (m-10) cc_final: 0.8893 (m-80) REVERT: H 114 LEU cc_start: 0.9352 (tp) cc_final: 0.9112 (tp) REVERT: H 117 MET cc_start: 0.8507 (tpt) cc_final: 0.7996 (tpt) REVERT: H 121 CYS cc_start: 0.8578 (m) cc_final: 0.8240 (m) REVERT: B 399 THR cc_start: 0.8618 (t) cc_final: 0.8197 (m) REVERT: B 402 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8576 (mp0) REVERT: B 405 TYR cc_start: 0.8365 (m-80) cc_final: 0.7682 (m-80) REVERT: B 756 GLN cc_start: 0.8891 (mt0) cc_final: 0.8683 (mt0) outliers start: 2 outliers final: 1 residues processed: 396 average time/residue: 0.0895 time to fit residues: 57.2666 Evaluate side-chains 311 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 128 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 185 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 188 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 127 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN B 709 ASN B 747 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.069849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.056480 restraints weight = 78149.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.057906 restraints weight = 54329.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.058960 restraints weight = 40948.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.059710 restraints weight = 32801.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.060275 restraints weight = 27678.858| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16799 Z= 0.131 Angle : 0.587 10.575 22853 Z= 0.304 Chirality : 0.041 0.244 2680 Planarity : 0.003 0.048 2866 Dihedral : 4.462 29.210 2428 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: -0.08 (0.18), residues: 2262 helix: 1.58 (0.14), residues: 1314 sheet: -1.82 (0.44), residues: 132 loop : -2.60 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 586 TYR 0.022 0.001 TYR C 732 PHE 0.029 0.002 PHE H 142 TRP 0.010 0.001 TRP G 178 HIS 0.003 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00273 (16791) covalent geometry : angle 0.58624 (22837) SS BOND : bond 0.00585 ( 8) SS BOND : angle 1.29588 ( 16) hydrogen bonds : bond 0.03606 ( 1098) hydrogen bonds : angle 4.53527 ( 3165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 THR cc_start: 0.8777 (t) cc_final: 0.8365 (t) REVERT: A 424 TYR cc_start: 0.9553 (t80) cc_final: 0.8961 (t80) REVERT: A 463 MET cc_start: 0.8806 (mtm) cc_final: 0.8102 (mpp) REVERT: A 466 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7411 (mt-10) REVERT: A 485 ARG cc_start: 0.9519 (mtt180) cc_final: 0.9100 (mtt180) REVERT: A 503 MET cc_start: 0.8091 (ttm) cc_final: 0.7049 (ptm) REVERT: A 527 MET cc_start: 0.8804 (mtm) cc_final: 0.8045 (mtt) REVERT: A 528 CYS cc_start: 0.9331 (m) cc_final: 0.9029 (m) REVERT: A 537 SER cc_start: 0.9680 (t) cc_final: 0.9233 (p) REVERT: A 657 GLU cc_start: 0.9041 (tp30) cc_final: 0.8743 (tp30) REVERT: C 399 THR cc_start: 0.8479 (t) cc_final: 0.8147 (t) REVERT: C 424 TYR cc_start: 0.9571 (t80) cc_final: 0.9012 (t80) REVERT: C 463 MET cc_start: 0.8275 (mpp) cc_final: 0.7936 (mpp) REVERT: C 466 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7632 (mt-10) REVERT: C 503 MET cc_start: 0.7959 (ttm) cc_final: 0.6909 (ptm) REVERT: C 527 MET cc_start: 0.8727 (mtm) cc_final: 0.7991 (mtt) REVERT: C 528 CYS cc_start: 0.9346 (m) cc_final: 0.9036 (m) REVERT: C 657 GLU cc_start: 0.9071 (tp30) cc_final: 0.8764 (tp30) REVERT: D 399 THR cc_start: 0.9082 (p) cc_final: 0.8580 (p) REVERT: D 402 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8324 (mm-30) REVERT: D 405 TYR cc_start: 0.8630 (m-80) cc_final: 0.7909 (m-80) REVERT: D 503 MET cc_start: 0.8860 (ttm) cc_final: 0.8268 (ttm) REVERT: D 518 LEU cc_start: 0.8678 (pp) cc_final: 0.8388 (tt) REVERT: D 587 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8776 (tp40) REVERT: D 708 MET cc_start: 0.8966 (mmt) cc_final: 0.8055 (mmt) REVERT: E 22 SER cc_start: 0.8747 (t) cc_final: 0.8471 (p) REVERT: E 142 PHE cc_start: 0.9441 (t80) cc_final: 0.9068 (t80) REVERT: E 181 TYR cc_start: 0.9245 (m-10) cc_final: 0.8977 (m-80) REVERT: F 112 VAL cc_start: 0.9737 (t) cc_final: 0.9519 (t) REVERT: F 114 LEU cc_start: 0.9298 (tp) cc_final: 0.9057 (tp) REVERT: F 115 LEU cc_start: 0.9669 (tp) cc_final: 0.9455 (tp) REVERT: F 117 MET cc_start: 0.8421 (tpt) cc_final: 0.7922 (tpt) REVERT: F 121 CYS cc_start: 0.8575 (m) cc_final: 0.8257 (m) REVERT: F 141 PHE cc_start: 0.7592 (m-10) cc_final: 0.6963 (m-80) REVERT: G 142 PHE cc_start: 0.9468 (t80) cc_final: 0.9052 (t80) REVERT: G 181 TYR cc_start: 0.9294 (m-10) cc_final: 0.9020 (m-80) REVERT: H 112 VAL cc_start: 0.9736 (t) cc_final: 0.9522 (t) REVERT: H 114 LEU cc_start: 0.9304 (tp) cc_final: 0.9068 (tp) REVERT: H 115 LEU cc_start: 0.9663 (tp) cc_final: 0.9453 (tp) REVERT: H 117 MET cc_start: 0.8438 (tpt) cc_final: 0.7950 (tpt) REVERT: H 121 CYS cc_start: 0.8616 (m) cc_final: 0.8297 (m) REVERT: H 141 PHE cc_start: 0.7611 (m-10) cc_final: 0.6980 (m-80) REVERT: B 402 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8407 (mp0) REVERT: B 405 TYR cc_start: 0.8529 (m-80) cc_final: 0.7865 (m-80) REVERT: B 463 MET cc_start: 0.8784 (mtt) cc_final: 0.8109 (mmm) REVERT: B 503 MET cc_start: 0.8854 (ttm) cc_final: 0.8138 (ttm) REVERT: B 541 PHE cc_start: 0.9099 (t80) cc_final: 0.8893 (t80) REVERT: B 587 GLN cc_start: 0.8998 (tp-100) cc_final: 0.8741 (tp40) REVERT: B 708 MET cc_start: 0.8962 (mmt) cc_final: 0.7987 (mmt) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.0844 time to fit residues: 56.3646 Evaluate side-chains 318 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 6 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 140 optimal weight: 0.0000 chunk 68 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 206 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS ** B 709 ASN ** 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 = 0.3167 r_free = 0.3167 target = 0.069138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.055637 restraints weight = 78940.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.057076 restraints weight = 54532.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.058113 restraints weight = 40975.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.058860 restraints weight = 32852.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.059422 restraints weight = 27716.063| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16799 Z= 0.158 Angle : 0.605 10.294 22853 Z= 0.316 Chirality : 0.041 0.191 2680 Planarity : 0.003 0.045 2866 Dihedral : 4.444 28.800 2428 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: -0.04 (0.18), residues: 2262 helix: 1.56 (0.14), residues: 1322 sheet: -1.77 (0.44), residues: 132 loop : -2.55 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 586 TYR 0.017 0.001 TYR B 797 PHE 0.027 0.002 PHE B 814 TRP 0.010 0.001 TRP B 578 HIS 0.003 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00327 (16791) covalent geometry : angle 0.60424 (22837) SS BOND : bond 0.00428 ( 8) SS BOND : angle 0.95296 ( 16) hydrogen bonds : bond 0.03581 ( 1098) hydrogen bonds : angle 4.53864 ( 3165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 THR cc_start: 0.8854 (t) cc_final: 0.8462 (t) REVERT: A 424 TYR cc_start: 0.9539 (t80) cc_final: 0.8927 (t80) REVERT: A 463 MET cc_start: 0.8787 (mtm) cc_final: 0.8095 (mpp) REVERT: A 466 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7471 (mt-10) REVERT: A 485 ARG cc_start: 0.9528 (mtt180) cc_final: 0.9125 (mtm180) REVERT: A 491 PHE cc_start: 0.8555 (m-80) cc_final: 0.8294 (m-80) REVERT: A 503 MET cc_start: 0.8088 (ttm) cc_final: 0.7537 (ttm) REVERT: A 527 MET cc_start: 0.8864 (mtm) cc_final: 0.7972 (mtt) REVERT: A 585 MET cc_start: 0.9370 (mmt) cc_final: 0.9030 (mmp) REVERT: A 657 GLU cc_start: 0.9026 (tp30) cc_final: 0.8708 (tp30) REVERT: C 399 THR cc_start: 0.8506 (t) cc_final: 0.8226 (t) REVERT: C 424 TYR cc_start: 0.9552 (t80) cc_final: 0.8979 (t80) REVERT: C 503 MET cc_start: 0.7959 (ttm) cc_final: 0.7133 (ptm) REVERT: C 504 ILE cc_start: 0.9371 (pt) cc_final: 0.9151 (pt) REVERT: C 527 MET cc_start: 0.8820 (mtm) cc_final: 0.8003 (mtt) REVERT: C 657 GLU cc_start: 0.9064 (tp30) cc_final: 0.8753 (tp30) REVERT: D 405 TYR cc_start: 0.8606 (m-80) cc_final: 0.7861 (m-80) REVERT: D 503 MET cc_start: 0.8935 (ttm) cc_final: 0.7966 (ttm) REVERT: D 587 GLN cc_start: 0.8973 (tp-100) cc_final: 0.8749 (tp40) REVERT: D 589 CYS cc_start: 0.8528 (t) cc_final: 0.8308 (t) REVERT: D 708 MET cc_start: 0.9090 (mmt) cc_final: 0.8255 (mmt) REVERT: E 22 SER cc_start: 0.8912 (t) cc_final: 0.8561 (p) REVERT: E 142 PHE cc_start: 0.9473 (t80) cc_final: 0.9041 (t80) REVERT: E 181 TYR cc_start: 0.9225 (m-10) cc_final: 0.8965 (m-80) REVERT: F 114 LEU cc_start: 0.9292 (tp) cc_final: 0.8950 (tp) REVERT: F 115 LEU cc_start: 0.9654 (tp) cc_final: 0.9427 (tp) REVERT: F 117 MET cc_start: 0.8429 (tpt) cc_final: 0.7954 (tpt) REVERT: F 121 CYS cc_start: 0.8532 (m) cc_final: 0.8210 (m) REVERT: F 141 PHE cc_start: 0.7673 (m-10) cc_final: 0.6890 (m-80) REVERT: F 191 GLU cc_start: 0.9322 (mp0) cc_final: 0.9081 (mp0) REVERT: G 142 PHE cc_start: 0.9459 (t80) cc_final: 0.9051 (t80) REVERT: G 181 TYR cc_start: 0.9270 (m-10) cc_final: 0.9003 (m-80) REVERT: G 200 MET cc_start: 0.9162 (ttm) cc_final: 0.8903 (mmm) REVERT: H 114 LEU cc_start: 0.9291 (tp) cc_final: 0.8956 (tp) REVERT: H 115 LEU cc_start: 0.9649 (tp) cc_final: 0.9428 (tp) REVERT: H 117 MET cc_start: 0.8433 (tpt) cc_final: 0.7944 (tpt) REVERT: H 121 CYS cc_start: 0.8535 (m) cc_final: 0.8209 (m) REVERT: H 141 PHE cc_start: 0.7699 (m-10) cc_final: 0.6915 (m-80) REVERT: H 191 GLU cc_start: 0.9323 (mp0) cc_final: 0.9105 (mp0) REVERT: B 402 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8453 (mp0) REVERT: B 405 TYR cc_start: 0.8538 (m-80) cc_final: 0.7794 (m-80) REVERT: B 503 MET cc_start: 0.8892 (ttm) cc_final: 0.7955 (ttm) REVERT: B 541 PHE cc_start: 0.9092 (t80) cc_final: 0.8820 (t80) REVERT: B 587 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8739 (tp40) REVERT: B 589 CYS cc_start: 0.8513 (t) cc_final: 0.8283 (t) REVERT: B 708 MET cc_start: 0.9052 (mmt) cc_final: 0.7916 (mmt) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.0872 time to fit residues: 57.1384 Evaluate side-chains 318 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 129 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 141 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** 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 = 0.3032 r_free = 0.3032 target = 0.063192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.050522 restraints weight = 84867.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.051701 restraints weight = 59191.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.052557 restraints weight = 45152.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.053146 restraints weight = 36624.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.053594 restraints weight = 31428.805| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 16799 Z= 0.452 Angle : 0.956 12.805 22853 Z= 0.520 Chirality : 0.049 0.200 2680 Planarity : 0.005 0.052 2866 Dihedral : 5.946 37.430 2428 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.13 % Allowed : 3.89 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.62 (0.17), residues: 2262 helix: 0.12 (0.13), residues: 1298 sheet: -2.28 (0.38), residues: 162 loop : -2.81 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 485 TYR 0.030 0.003 TYR D 533 PHE 0.042 0.004 PHE C 546 TRP 0.018 0.003 TRP A 526 HIS 0.010 0.003 HIS H 199 Details of bonding type rmsd covalent geometry : bond 0.00901 (16791) covalent geometry : angle 0.95605 (22837) SS BOND : bond 0.00603 ( 8) SS BOND : angle 1.19738 ( 16) hydrogen bonds : bond 0.05566 ( 1098) hydrogen bonds : angle 6.00099 ( 3165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 333 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 PHE cc_start: 0.8796 (m-80) cc_final: 0.8452 (m-80) REVERT: A 496 MET cc_start: 0.9192 (tpt) cc_final: 0.8978 (tpp) REVERT: A 503 MET cc_start: 0.8766 (ttm) cc_final: 0.8496 (ttm) REVERT: A 527 MET cc_start: 0.9077 (mtm) cc_final: 0.8633 (mtt) REVERT: A 592 SER cc_start: 0.8830 (p) cc_final: 0.8462 (m) REVERT: A 657 GLU cc_start: 0.9066 (tp30) cc_final: 0.8691 (tp30) REVERT: A 726 ASN cc_start: 0.9273 (m-40) cc_final: 0.8868 (t0) REVERT: A 799 LEU cc_start: 0.9473 (tp) cc_final: 0.9266 (tp) REVERT: C 496 MET cc_start: 0.9190 (tpt) cc_final: 0.8961 (tpp) REVERT: C 503 MET cc_start: 0.8595 (ttm) cc_final: 0.8300 (ttm) REVERT: C 527 MET cc_start: 0.9055 (mtm) cc_final: 0.8602 (mtt) REVERT: C 592 SER cc_start: 0.8957 (p) cc_final: 0.8528 (m) REVERT: C 657 GLU cc_start: 0.9101 (tp30) cc_final: 0.8741 (tp30) REVERT: C 726 ASN cc_start: 0.9283 (m-40) cc_final: 0.8934 (t0) REVERT: C 755 GLU cc_start: 0.9098 (mp0) cc_final: 0.8863 (pm20) REVERT: C 799 LEU cc_start: 0.9440 (tp) cc_final: 0.9238 (tp) REVERT: D 399 THR cc_start: 0.8752 (p) cc_final: 0.8191 (p) REVERT: D 405 TYR cc_start: 0.8457 (m-80) cc_final: 0.7927 (m-80) REVERT: D 503 MET cc_start: 0.9145 (ttm) cc_final: 0.8544 (ttm) REVERT: D 517 PHE cc_start: 0.9111 (t80) cc_final: 0.8397 (t80) REVERT: D 518 LEU cc_start: 0.9463 (pt) cc_final: 0.9153 (pt) REVERT: E 22 SER cc_start: 0.8969 (t) cc_final: 0.8477 (p) REVERT: E 23 LEU cc_start: 0.8435 (mm) cc_final: 0.8047 (mm) REVERT: E 142 PHE cc_start: 0.9664 (t80) cc_final: 0.9435 (t80) REVERT: F 114 LEU cc_start: 0.9340 (tp) cc_final: 0.9043 (tp) REVERT: F 115 LEU cc_start: 0.9663 (tp) cc_final: 0.9446 (tp) REVERT: F 117 MET cc_start: 0.8509 (tpt) cc_final: 0.8019 (tpt) REVERT: F 121 CYS cc_start: 0.8654 (m) cc_final: 0.8443 (m) REVERT: F 141 PHE cc_start: 0.7726 (m-10) cc_final: 0.6986 (m-80) REVERT: G 23 LEU cc_start: 0.8431 (mm) cc_final: 0.8141 (mm) REVERT: G 142 PHE cc_start: 0.9669 (t80) cc_final: 0.9454 (t80) REVERT: H 114 LEU cc_start: 0.9339 (tp) cc_final: 0.9067 (tp) REVERT: H 115 LEU cc_start: 0.9671 (tp) cc_final: 0.9450 (tp) REVERT: H 117 MET cc_start: 0.8506 (tpt) cc_final: 0.7995 (tpt) REVERT: H 121 CYS cc_start: 0.8656 (m) cc_final: 0.8426 (m) REVERT: B 405 TYR cc_start: 0.8493 (m-80) cc_final: 0.7936 (m-80) REVERT: B 517 PHE cc_start: 0.9139 (t80) cc_final: 0.8512 (t80) outliers start: 2 outliers final: 0 residues processed: 333 average time/residue: 0.0914 time to fit residues: 51.2805 Evaluate side-chains 258 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 66 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 216 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 9 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.069821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.056616 restraints weight = 77465.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.058026 restraints weight = 54246.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.059068 restraints weight = 40827.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.059827 restraints weight = 32750.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.060150 restraints weight = 27586.877| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16799 Z= 0.125 Angle : 0.636 11.563 22853 Z= 0.328 Chirality : 0.042 0.230 2680 Planarity : 0.003 0.056 2866 Dihedral : 4.707 33.182 2428 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.19 (0.18), residues: 2262 helix: 1.45 (0.14), residues: 1304 sheet: -1.84 (0.45), residues: 132 loop : -2.54 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 586 TYR 0.018 0.001 TYR D 797 PHE 0.031 0.002 PHE F 142 TRP 0.021 0.001 TRP D 605 HIS 0.005 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00259 (16791) covalent geometry : angle 0.63540 (22837) SS BOND : bond 0.00672 ( 8) SS BOND : angle 0.92271 ( 16) hydrogen bonds : bond 0.03735 ( 1098) hydrogen bonds : angle 4.59911 ( 3165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 TYR cc_start: 0.9540 (t80) cc_final: 0.8817 (t80) REVERT: A 485 ARG cc_start: 0.9495 (mtt180) cc_final: 0.9137 (mtm180) REVERT: A 503 MET cc_start: 0.8402 (ttm) cc_final: 0.8178 (ttm) REVERT: A 527 MET cc_start: 0.8863 (mtm) cc_final: 0.8423 (mtt) REVERT: A 540 LEU cc_start: 0.9777 (mm) cc_final: 0.9552 (mm) REVERT: A 657 GLU cc_start: 0.9012 (tp30) cc_final: 0.8664 (tp30) REVERT: A 732 TYR cc_start: 0.5722 (m-80) cc_final: 0.5484 (m-10) REVERT: A 799 LEU cc_start: 0.9424 (tp) cc_final: 0.9212 (tp) REVERT: C 399 THR cc_start: 0.8630 (t) cc_final: 0.8146 (t) REVERT: C 424 TYR cc_start: 0.9508 (t80) cc_final: 0.8810 (t80) REVERT: C 504 ILE cc_start: 0.9287 (pt) cc_final: 0.9083 (pt) REVERT: C 527 MET cc_start: 0.8837 (mtm) cc_final: 0.8024 (mtt) REVERT: C 528 CYS cc_start: 0.9281 (m) cc_final: 0.8904 (m) REVERT: C 537 SER cc_start: 0.9738 (t) cc_final: 0.9234 (p) REVERT: C 541 PHE cc_start: 0.8727 (t80) cc_final: 0.8341 (t80) REVERT: C 657 GLU cc_start: 0.8991 (tp30) cc_final: 0.8662 (tp30) REVERT: C 799 LEU cc_start: 0.9399 (tp) cc_final: 0.9189 (tp) REVERT: D 405 TYR cc_start: 0.8634 (m-80) cc_final: 0.7798 (m-80) REVERT: D 485 ARG cc_start: 0.9356 (ptp-170) cc_final: 0.8938 (ptp-170) REVERT: D 503 MET cc_start: 0.8925 (ttm) cc_final: 0.8411 (ttm) REVERT: D 518 LEU cc_start: 0.8938 (pt) cc_final: 0.8592 (pt) REVERT: D 587 GLN cc_start: 0.8924 (tp-100) cc_final: 0.8634 (tp40) REVERT: D 708 MET cc_start: 0.9078 (mmt) cc_final: 0.8435 (mmt) REVERT: E 22 SER cc_start: 0.8877 (t) cc_final: 0.8534 (p) REVERT: E 142 PHE cc_start: 0.9349 (t80) cc_final: 0.9090 (t80) REVERT: F 114 LEU cc_start: 0.9310 (tp) cc_final: 0.8992 (tp) REVERT: F 115 LEU cc_start: 0.9644 (tp) cc_final: 0.9418 (tp) REVERT: F 117 MET cc_start: 0.8437 (tpt) cc_final: 0.7977 (tpt) REVERT: F 141 PHE cc_start: 0.7526 (m-10) cc_final: 0.6871 (m-80) REVERT: F 191 GLU cc_start: 0.9336 (mp0) cc_final: 0.8896 (mp0) REVERT: G 142 PHE cc_start: 0.9327 (t80) cc_final: 0.9041 (t80) REVERT: H 114 LEU cc_start: 0.9310 (tp) cc_final: 0.8985 (tp) REVERT: H 115 LEU cc_start: 0.9629 (tp) cc_final: 0.9420 (tp) REVERT: H 117 MET cc_start: 0.8426 (tpt) cc_final: 0.7949 (tpt) REVERT: H 141 PHE cc_start: 0.7543 (m-10) cc_final: 0.6888 (m-80) REVERT: H 191 GLU cc_start: 0.9344 (mp0) cc_final: 0.8879 (mp0) REVERT: B 405 TYR cc_start: 0.8543 (m-80) cc_final: 0.7783 (m-80) REVERT: B 503 MET cc_start: 0.8980 (ttm) cc_final: 0.8381 (ttm) REVERT: B 541 PHE cc_start: 0.9107 (t80) cc_final: 0.8730 (t80) REVERT: B 587 GLN cc_start: 0.8920 (tp-100) cc_final: 0.8644 (tp40) REVERT: B 613 ILE cc_start: 0.9571 (pt) cc_final: 0.9296 (mp) REVERT: B 708 MET cc_start: 0.9097 (mmt) cc_final: 0.8462 (mmt) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.1008 time to fit residues: 69.2228 Evaluate side-chains 313 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 151 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 196 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS C 412 HIS D 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.064157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.051913 restraints weight = 83520.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.052999 restraints weight = 60788.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.053799 restraints weight = 44135.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.054287 restraints weight = 38090.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.054404 restraints weight = 33256.042| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 16799 Z= 0.387 Angle : 0.874 11.061 22853 Z= 0.473 Chirality : 0.046 0.306 2680 Planarity : 0.005 0.051 2866 Dihedral : 5.654 34.846 2428 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.82 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.32 (0.17), residues: 2262 helix: 0.45 (0.14), residues: 1300 sheet: -2.27 (0.38), residues: 164 loop : -2.83 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 675 TYR 0.028 0.003 TYR B 797 PHE 0.060 0.004 PHE C 541 TRP 0.030 0.003 TRP D 605 HIS 0.006 0.002 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00774 (16791) covalent geometry : angle 0.87361 (22837) SS BOND : bond 0.00490 ( 8) SS BOND : angle 0.98614 ( 16) hydrogen bonds : bond 0.05003 ( 1098) hydrogen bonds : angle 5.64795 ( 3165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 TYR cc_start: 0.8440 (m-10) cc_final: 0.8222 (m-10) REVERT: A 527 MET cc_start: 0.8999 (mtm) cc_final: 0.8403 (mtp) REVERT: A 592 SER cc_start: 0.8746 (p) cc_final: 0.8325 (m) REVERT: A 657 GLU cc_start: 0.8996 (tp30) cc_final: 0.8600 (tp30) REVERT: A 721 MET cc_start: 0.8988 (mtm) cc_final: 0.8677 (mtm) REVERT: A 726 ASN cc_start: 0.9060 (m-40) cc_final: 0.8747 (t0) REVERT: A 799 LEU cc_start: 0.9514 (tp) cc_final: 0.9306 (tp) REVERT: C 504 ILE cc_start: 0.9445 (pt) cc_final: 0.9192 (pt) REVERT: C 527 MET cc_start: 0.9091 (mtm) cc_final: 0.8660 (mtt) REVERT: C 657 GLU cc_start: 0.9013 (tp30) cc_final: 0.8651 (tp30) REVERT: C 799 LEU cc_start: 0.9495 (tp) cc_final: 0.9255 (tp) REVERT: C 809 VAL cc_start: 0.9571 (p) cc_final: 0.9283 (m) REVERT: D 405 TYR cc_start: 0.8498 (m-80) cc_final: 0.7874 (m-80) REVERT: E 22 SER cc_start: 0.8865 (t) cc_final: 0.8562 (p) REVERT: E 142 PHE cc_start: 0.9552 (t80) cc_final: 0.9235 (t80) REVERT: F 114 LEU cc_start: 0.9345 (tp) cc_final: 0.9024 (tp) REVERT: F 115 LEU cc_start: 0.9657 (tp) cc_final: 0.9403 (tp) REVERT: F 141 PHE cc_start: 0.7523 (m-10) cc_final: 0.6902 (m-80) REVERT: F 151 ILE cc_start: 0.9845 (mt) cc_final: 0.9597 (mt) REVERT: G 142 PHE cc_start: 0.9566 (t80) cc_final: 0.9162 (t80) REVERT: H 114 LEU cc_start: 0.9346 (tp) cc_final: 0.9025 (tp) REVERT: H 115 LEU cc_start: 0.9663 (tp) cc_final: 0.9416 (tp) REVERT: H 141 PHE cc_start: 0.7484 (m-10) cc_final: 0.6880 (m-80) REVERT: H 151 ILE cc_start: 0.9849 (mt) cc_final: 0.9594 (mt) REVERT: H 191 GLU cc_start: 0.9319 (mp0) cc_final: 0.9091 (mp0) REVERT: B 399 THR cc_start: 0.8774 (p) cc_final: 0.8177 (p) REVERT: B 405 TYR cc_start: 0.8523 (m-80) cc_final: 0.7798 (m-80) REVERT: B 503 MET cc_start: 0.9080 (ttm) cc_final: 0.8611 (ttp) REVERT: B 518 LEU cc_start: 0.9528 (pt) cc_final: 0.9203 (pt) REVERT: B 541 PHE cc_start: 0.9111 (t80) cc_final: 0.8861 (t80) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.1019 time to fit residues: 55.9308 Evaluate side-chains 251 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 76 optimal weight: 0.0020 chunk 116 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 18 optimal weight: 0.0770 chunk 183 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 170 optimal weight: 7.9990 chunk 182 optimal weight: 0.3980 chunk 194 optimal weight: 0.9980 overall best weight: 0.3746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.070961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.057584 restraints weight = 77472.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.059015 restraints weight = 54173.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.060055 restraints weight = 41210.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.060763 restraints weight = 33296.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.061374 restraints weight = 28360.381| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16799 Z= 0.123 Angle : 0.652 11.761 22853 Z= 0.332 Chirality : 0.042 0.214 2680 Planarity : 0.003 0.058 2866 Dihedral : 4.615 31.293 2428 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.08 (0.18), residues: 2262 helix: 1.58 (0.14), residues: 1306 sheet: -1.70 (0.44), residues: 144 loop : -2.61 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 586 TYR 0.016 0.001 TYR C 405 PHE 0.032 0.002 PHE C 541 TRP 0.016 0.001 TRP C 671 HIS 0.007 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00247 (16791) covalent geometry : angle 0.65142 (22837) SS BOND : bond 0.00425 ( 8) SS BOND : angle 0.78670 ( 16) hydrogen bonds : bond 0.03630 ( 1098) hydrogen bonds : angle 4.45900 ( 3165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 THR cc_start: 0.8754 (t) cc_final: 0.8355 (t) REVERT: A 485 ARG cc_start: 0.9345 (mtt180) cc_final: 0.8925 (mtm180) REVERT: A 503 MET cc_start: 0.8367 (ttp) cc_final: 0.7633 (ptm) REVERT: A 527 MET cc_start: 0.8762 (mtm) cc_final: 0.8399 (mtt) REVERT: A 657 GLU cc_start: 0.8967 (tp30) cc_final: 0.8653 (tp30) REVERT: A 799 LEU cc_start: 0.9441 (tp) cc_final: 0.9214 (tp) REVERT: C 424 TYR cc_start: 0.9514 (t80) cc_final: 0.9256 (t80) REVERT: C 485 ARG cc_start: 0.9509 (mmm-85) cc_final: 0.9153 (mtt180) REVERT: C 527 MET cc_start: 0.8810 (mtm) cc_final: 0.8346 (mtt) REVERT: C 528 CYS cc_start: 0.9093 (m) cc_final: 0.8693 (m) REVERT: C 657 GLU cc_start: 0.8981 (tp30) cc_final: 0.8685 (tp30) REVERT: C 799 LEU cc_start: 0.9392 (tp) cc_final: 0.9150 (tp) REVERT: C 809 VAL cc_start: 0.9515 (p) cc_final: 0.9273 (m) REVERT: D 405 TYR cc_start: 0.8648 (m-80) cc_final: 0.7879 (m-80) REVERT: D 485 ARG cc_start: 0.9291 (ptp-170) cc_final: 0.8937 (ptp-170) REVERT: D 503 MET cc_start: 0.8896 (ttm) cc_final: 0.8213 (ttm) REVERT: D 517 PHE cc_start: 0.8929 (t80) cc_final: 0.8635 (t80) REVERT: D 518 LEU cc_start: 0.9053 (pt) cc_final: 0.8515 (pt) REVERT: D 587 GLN cc_start: 0.8802 (tp-100) cc_final: 0.8528 (tp40) REVERT: D 702 TYR cc_start: 0.9624 (t80) cc_final: 0.9339 (t80) REVERT: D 708 MET cc_start: 0.9077 (mmt) cc_final: 0.8537 (mmt) REVERT: E 22 SER cc_start: 0.8814 (t) cc_final: 0.8502 (p) REVERT: E 142 PHE cc_start: 0.9320 (t80) cc_final: 0.8952 (t80) REVERT: F 114 LEU cc_start: 0.9312 (tp) cc_final: 0.8941 (tp) REVERT: F 115 LEU cc_start: 0.9622 (tp) cc_final: 0.9404 (tp) REVERT: F 117 MET cc_start: 0.8382 (tpt) cc_final: 0.7911 (tpt) REVERT: F 140 ILE cc_start: 0.9089 (pt) cc_final: 0.8672 (pt) REVERT: F 141 PHE cc_start: 0.7413 (m-10) cc_final: 0.6732 (m-80) REVERT: G 142 PHE cc_start: 0.9365 (t80) cc_final: 0.9022 (t80) REVERT: H 114 LEU cc_start: 0.9304 (tp) cc_final: 0.8921 (tp) REVERT: H 117 MET cc_start: 0.8377 (tpt) cc_final: 0.7921 (tpt) REVERT: H 140 ILE cc_start: 0.9046 (pt) cc_final: 0.8696 (pt) REVERT: H 141 PHE cc_start: 0.7415 (m-10) cc_final: 0.6735 (m-80) REVERT: H 191 GLU cc_start: 0.9221 (mp0) cc_final: 0.8964 (mp0) REVERT: B 405 TYR cc_start: 0.8564 (m-80) cc_final: 0.7800 (m-80) REVERT: B 485 ARG cc_start: 0.9297 (ptp-170) cc_final: 0.8960 (ptp-170) REVERT: B 503 MET cc_start: 0.8910 (ttm) cc_final: 0.8192 (ttm) REVERT: B 517 PHE cc_start: 0.8991 (t80) cc_final: 0.8692 (t80) REVERT: B 518 LEU cc_start: 0.8986 (pt) cc_final: 0.8456 (pt) REVERT: B 541 PHE cc_start: 0.9091 (t80) cc_final: 0.8677 (t80) REVERT: B 587 GLN cc_start: 0.8803 (tp-100) cc_final: 0.8548 (tp40) REVERT: B 708 MET cc_start: 0.9070 (mmt) cc_final: 0.8532 (mmt) outliers start: 0 outliers final: 0 residues processed: 415 average time/residue: 0.1102 time to fit residues: 73.8559 Evaluate side-chains 310 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 110 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 207 optimal weight: 0.4980 chunk 127 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.069721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.056524 restraints weight = 77859.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.057904 restraints weight = 54562.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.058891 restraints weight = 41570.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.059560 restraints weight = 33557.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.060104 restraints weight = 28627.601| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16799 Z= 0.138 Angle : 0.642 11.293 22853 Z= 0.328 Chirality : 0.041 0.225 2680 Planarity : 0.003 0.048 2866 Dihedral : 4.521 28.085 2428 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.06 (0.18), residues: 2262 helix: 1.71 (0.15), residues: 1304 sheet: -1.94 (0.39), residues: 168 loop : -2.47 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 675 TYR 0.015 0.001 TYR C 732 PHE 0.031 0.002 PHE C 607 TRP 0.013 0.001 TRP A 671 HIS 0.004 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00294 (16791) covalent geometry : angle 0.64207 (22837) SS BOND : bond 0.00409 ( 8) SS BOND : angle 0.72349 ( 16) hydrogen bonds : bond 0.03529 ( 1098) hydrogen bonds : angle 4.45598 ( 3165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 THR cc_start: 0.8795 (t) cc_final: 0.8573 (t) REVERT: A 485 ARG cc_start: 0.9318 (mtt180) cc_final: 0.8917 (mtt180) REVERT: A 491 PHE cc_start: 0.8096 (m-10) cc_final: 0.7850 (m-10) REVERT: A 527 MET cc_start: 0.8773 (mtm) cc_final: 0.8269 (mtt) REVERT: A 657 GLU cc_start: 0.8936 (tp30) cc_final: 0.8573 (tp30) REVERT: A 674 MET cc_start: 0.8640 (mpp) cc_final: 0.7844 (ptp) REVERT: A 704 LEU cc_start: 0.9447 (tp) cc_final: 0.9229 (tp) REVERT: A 728 ASP cc_start: 0.8849 (p0) cc_final: 0.8523 (p0) REVERT: A 732 TYR cc_start: 0.5993 (m-80) cc_final: 0.5734 (m-80) REVERT: A 755 GLU cc_start: 0.9341 (mp0) cc_final: 0.9080 (pm20) REVERT: A 799 LEU cc_start: 0.9449 (tp) cc_final: 0.9113 (tp) REVERT: A 809 VAL cc_start: 0.9513 (p) cc_final: 0.9249 (m) REVERT: C 399 THR cc_start: 0.8715 (t) cc_final: 0.8488 (t) REVERT: C 424 TYR cc_start: 0.9478 (t80) cc_final: 0.9254 (t80) REVERT: C 524 GLU cc_start: 0.9336 (pm20) cc_final: 0.8929 (pm20) REVERT: C 527 MET cc_start: 0.8767 (mtm) cc_final: 0.8121 (mtt) REVERT: C 657 GLU cc_start: 0.8969 (tp30) cc_final: 0.8652 (tp30) REVERT: C 704 LEU cc_start: 0.9250 (tp) cc_final: 0.9009 (tp) REVERT: C 799 LEU cc_start: 0.9437 (tp) cc_final: 0.9094 (tp) REVERT: C 809 VAL cc_start: 0.9515 (p) cc_final: 0.9299 (m) REVERT: D 405 TYR cc_start: 0.8706 (m-80) cc_final: 0.7930 (m-80) REVERT: D 486 GLU cc_start: 0.9460 (mp0) cc_final: 0.9178 (mp0) REVERT: D 503 MET cc_start: 0.8891 (ttm) cc_final: 0.8248 (ttm) REVERT: D 517 PHE cc_start: 0.9031 (t80) cc_final: 0.8587 (t80) REVERT: D 518 LEU cc_start: 0.9022 (pt) cc_final: 0.8176 (pt) REVERT: D 541 PHE cc_start: 0.8936 (t80) cc_final: 0.8634 (t80) REVERT: D 581 LEU cc_start: 0.9298 (tp) cc_final: 0.8996 (tt) REVERT: D 702 TYR cc_start: 0.9676 (t80) cc_final: 0.9354 (t80) REVERT: D 708 MET cc_start: 0.8946 (mmt) cc_final: 0.8446 (mmt) REVERT: E 22 SER cc_start: 0.8825 (t) cc_final: 0.8520 (p) REVERT: E 142 PHE cc_start: 0.9406 (t80) cc_final: 0.8930 (t80) REVERT: F 114 LEU cc_start: 0.9272 (tp) cc_final: 0.8976 (tp) REVERT: F 115 LEU cc_start: 0.9648 (tp) cc_final: 0.9383 (tp) REVERT: F 117 MET cc_start: 0.8392 (tpt) cc_final: 0.7913 (tpt) REVERT: F 141 PHE cc_start: 0.7419 (m-10) cc_final: 0.6730 (m-80) REVERT: G 142 PHE cc_start: 0.9423 (t80) cc_final: 0.9000 (t80) REVERT: H 114 LEU cc_start: 0.9273 (tp) cc_final: 0.8964 (tp) REVERT: H 115 LEU cc_start: 0.9645 (tp) cc_final: 0.9437 (tp) REVERT: H 117 MET cc_start: 0.8388 (tpt) cc_final: 0.7928 (tpt) REVERT: H 140 ILE cc_start: 0.9151 (pt) cc_final: 0.8675 (pt) REVERT: H 141 PHE cc_start: 0.7381 (m-10) cc_final: 0.6677 (m-80) REVERT: B 405 TYR cc_start: 0.8659 (m-80) cc_final: 0.7913 (m-80) REVERT: B 485 ARG cc_start: 0.9144 (ptp-170) cc_final: 0.8846 (ptp-170) REVERT: B 503 MET cc_start: 0.8893 (ttm) cc_final: 0.8172 (ttm) REVERT: B 517 PHE cc_start: 0.9109 (t80) cc_final: 0.8664 (t80) REVERT: B 518 LEU cc_start: 0.9089 (pt) cc_final: 0.8248 (pt) REVERT: B 541 PHE cc_start: 0.9092 (t80) cc_final: 0.8710 (t80) REVERT: B 581 LEU cc_start: 0.9280 (tp) cc_final: 0.8995 (tt) REVERT: B 702 TYR cc_start: 0.9687 (t80) cc_final: 0.9370 (t80) REVERT: B 708 MET cc_start: 0.8939 (mmt) cc_final: 0.8314 (mmt) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.1021 time to fit residues: 64.4874 Evaluate side-chains 305 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 18 optimal weight: 0.0370 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 chunk 123 optimal weight: 40.0000 chunk 12 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 24 optimal weight: 0.0670 chunk 81 optimal weight: 0.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 435 HIS D 709 ASN B 435 HIS B 709 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.072235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.058949 restraints weight = 76339.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.060345 restraints weight = 53826.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.061330 restraints weight = 41146.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.062020 restraints weight = 33439.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.062587 restraints weight = 28469.604| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16799 Z= 0.112 Angle : 0.636 10.968 22853 Z= 0.317 Chirality : 0.042 0.259 2680 Planarity : 0.003 0.053 2866 Dihedral : 4.232 26.310 2428 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.29 (0.18), residues: 2262 helix: 1.83 (0.15), residues: 1312 sheet: -1.50 (0.43), residues: 152 loop : -2.40 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 675 TYR 0.016 0.001 TYR A 424 PHE 0.030 0.001 PHE B 814 TRP 0.015 0.001 TRP A 671 HIS 0.006 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00234 (16791) covalent geometry : angle 0.63570 (22837) SS BOND : bond 0.00370 ( 8) SS BOND : angle 0.73249 ( 16) hydrogen bonds : bond 0.03295 ( 1098) hydrogen bonds : angle 4.25477 ( 3165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2328.76 seconds wall clock time: 41 minutes 20.06 seconds (2480.06 seconds total)