Starting phenix.real_space_refine on Sat Dec 9 13:03:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n52_0346/12_2023/6n52_0346.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n52_0346/12_2023/6n52_0346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n52_0346/12_2023/6n52_0346.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n52_0346/12_2023/6n52_0346.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n52_0346/12_2023/6n52_0346.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n52_0346/12_2023/6n52_0346.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 108 5.16 5 C 7096 2.51 5 N 1878 2.21 5 O 2026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11108 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5526 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 740} Chain breaks: 2 Unresolved non-hydrogen bonds: 598 Unresolved non-hydrogen angles: 743 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 6, 'GLU:plan': 20, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 325 Chain: "B" Number of atoms: 5526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5526 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 740} Chain breaks: 2 Unresolved non-hydrogen bonds: 598 Unresolved non-hydrogen angles: 743 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 6, 'GLU:plan': 20, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 325 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.28, per 1000 atoms: 0.57 Number of scatterers: 11108 At special positions: 0 Unit cell: (117.66, 79.5, 183.38, 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 108 16.00 O 2026 8.00 N 1878 7.00 C 7096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.04 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.03 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied NAG-ASN " NAG A 901 " - " ASN A 210 " " NAG A 902 " - " ASN A 445 " " NAG B 901 " - " ASN B 210 " " NAG B 902 " - " ASN B 445 " Time building additional restraints: 4.07 Conformation dependent library (CDL) restraints added in 2.2 seconds 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2892 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 47.8% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.945A pdb=" N VAL A 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 81 Processing helix chain 'A' and resid 101 through 122 Processing helix chain 'A' and resid 151 through 163 removed outlier: 4.120A pdb=" N GLN A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN A 160 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 195 through 210 removed outlier: 3.706A pdb=" N VAL A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 236 removed outlier: 3.645A pdb=" N SER A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 227 " --> pdb=" O TYR A 223 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 279 through 294 Processing helix chain 'A' and resid 305 through 308 removed outlier: 3.609A pdb=" N ALA A 308 " --> pdb=" O ASP A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 305 through 308' Processing helix chain 'A' and resid 334 through 343 removed outlier: 3.540A pdb=" N ASP A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 363 removed outlier: 3.729A pdb=" N PHE A 363 " --> pdb=" O TRP A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 419 removed outlier: 3.708A pdb=" N VAL A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 434 through 443 removed outlier: 3.819A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 598 removed outlier: 3.988A pdb=" N ALA A 582 " --> pdb=" O PRO A 578 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA A 583 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 612 removed outlier: 3.689A pdb=" N SER A 612 " --> pdb=" O PRO A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 636 removed outlier: 4.044A pdb=" N THR A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 668 removed outlier: 4.082A pdb=" N GLY A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE A 651 " --> pdb=" O GLN A 647 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY A 652 " --> pdb=" O ARG A 648 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) Proline residue: A 655 - end of helix removed outlier: 3.663A pdb=" N SER A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 662 " --> pdb=" O SER A 658 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 715 removed outlier: 4.243A pdb=" N ALA A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET A 714 " --> pdb=" O ALA A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 761 Proline residue: A 743 - end of helix removed outlier: 3.594A pdb=" N TYR A 746 " --> pdb=" O THR A 742 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 794 removed outlier: 6.264A pdb=" N ALA A 771 " --> pdb=" O ASN A 767 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR A 780 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 783 " --> pdb=" O TYR A 779 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 786 " --> pdb=" O CYS A 782 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL A 789 " --> pdb=" O TRP A 785 " (cutoff:3.500A) Proline residue: A 790 - end of helix Processing helix chain 'A' and resid 799 through 816 removed outlier: 3.757A pdb=" N VAL A 806 " --> pdb=" O MET A 802 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A 807 " --> pdb=" O CYS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 832 removed outlier: 3.698A pdb=" N ARG A 831 " --> pdb=" O LYS A 828 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN A 832 " --> pdb=" O PRO A 829 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 828 through 832' Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.944A pdb=" N VAL B 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 81 Processing helix chain 'B' and resid 101 through 122 Processing helix chain 'B' and resid 151 through 163 removed outlier: 4.119A pdb=" N GLN B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN B 160 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 195 through 210 removed outlier: 3.707A pdb=" N VAL B 206 " --> pdb=" O MET B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 236 removed outlier: 3.644A pdb=" N SER B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 227 " --> pdb=" O TYR B 223 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 279 through 294 Processing helix chain 'B' and resid 305 through 308 removed outlier: 3.609A pdb=" N ALA B 308 " --> pdb=" O ASP B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 305 through 308' Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.541A pdb=" N ASP B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 363 removed outlier: 3.729A pdb=" N PHE B 363 " --> pdb=" O TRP B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 419 removed outlier: 3.707A pdb=" N VAL B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 401 " --> pdb=" O MET B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 434 through 443 removed outlier: 3.818A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 598 removed outlier: 3.988A pdb=" N ALA B 582 " --> pdb=" O PRO B 578 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA B 583 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 removed outlier: 3.689A pdb=" N SER B 612 " --> pdb=" O PRO B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 636 removed outlier: 4.045A pdb=" N THR B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 668 removed outlier: 4.082A pdb=" N GLY B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE B 651 " --> pdb=" O GLN B 647 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 653 " --> pdb=" O ILE B 649 " (cutoff:3.500A) Proline residue: B 655 - end of helix removed outlier: 3.664A pdb=" N SER B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 662 " --> pdb=" O SER B 658 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 715 removed outlier: 4.244A pdb=" N ALA B 697 " --> pdb=" O GLN B 693 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET B 714 " --> pdb=" O ALA B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 761 Proline residue: B 743 - end of helix removed outlier: 3.595A pdb=" N TYR B 746 " --> pdb=" O THR B 742 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 794 removed outlier: 6.265A pdb=" N ALA B 771 " --> pdb=" O ASN B 767 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B 773 " --> pdb=" O ASN B 769 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR B 780 " --> pdb=" O PHE B 776 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B 783 " --> pdb=" O TYR B 779 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 786 " --> pdb=" O CYS B 782 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL B 789 " --> pdb=" O TRP B 785 " (cutoff:3.500A) Proline residue: B 790 - end of helix Processing helix chain 'B' and resid 799 through 816 removed outlier: 3.758A pdb=" N VAL B 806 " --> pdb=" O MET B 802 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER B 807 " --> pdb=" O CYS B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 832 removed outlier: 3.697A pdb=" N ARG B 831 " --> pdb=" O LYS B 828 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN B 832 " --> pdb=" O PRO B 829 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 828 through 832' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.801A pdb=" N GLU A 94 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 41 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE A 36 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY A 145 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ILE A 170 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 242 removed outlier: 9.831A pdb=" N TYR A 246 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ALA A 216 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ILE A 248 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N HIS A 218 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 241 through 242 removed outlier: 6.008A pdb=" N VAL A 273 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 277 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR A 219 " --> pdb=" O PHE A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 329 removed outlier: 3.582A pdb=" N TRP A 487 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ASN A 470 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASN A 483 " --> pdb=" O ASN A 470 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LYS A 472 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N TYR A 481 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 447 removed outlier: 3.686A pdb=" N PHE A 446 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 520 through 521 Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AA9, first strand: chain 'A' and resid 556 through 557 Processing sheet with id=AB1, first strand: chain 'A' and resid 719 through 720 Processing sheet with id=AB2, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.801A pdb=" N GLU B 94 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 41 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE B 36 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY B 145 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ILE B 170 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 241 through 242 removed outlier: 9.831A pdb=" N TYR B 246 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ALA B 216 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N ILE B 248 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N HIS B 218 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 241 through 242 removed outlier: 6.008A pdb=" N VAL B 273 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 277 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR B 219 " --> pdb=" O PHE B 277 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 325 through 329 removed outlier: 3.582A pdb=" N TRP B 487 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASN B 470 " --> pdb=" O ASN B 483 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASN B 483 " --> pdb=" O ASN B 470 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LYS B 472 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR B 481 " --> pdb=" O LYS B 472 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 365 through 366 Processing sheet with id=AB7, first strand: chain 'B' and resid 445 through 447 removed outlier: 3.685A pdb=" N PHE B 446 " --> pdb=" O ILE B 454 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 520 through 521 Processing sheet with id=AB9, first strand: chain 'B' and resid 541 through 543 Processing sheet with id=AC1, first strand: chain 'B' and resid 556 through 557 Processing sheet with id=AC2, first strand: chain 'B' and resid 719 through 720 526 hydrogen bonds defined for protein. 1512 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: 3.43 Time building geometry restraints manager: 4.45 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: 3598 1.34 - 1.46: 2698 1.46 - 1.58: 4910 1.58 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 11358 Sorted by residual: bond pdb=" C SER A 654 " pdb=" N PRO A 655 " ideal model delta sigma weight residual 1.337 1.365 -0.028 1.24e-02 6.50e+03 4.94e+00 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.84e+00 bond pdb=" C SER B 654 " pdb=" N PRO B 655 " ideal model delta sigma weight residual 1.337 1.364 -0.027 1.24e-02 6.50e+03 4.82e+00 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C1 NAG A 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.01e+00 ... (remaining 11353 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.81: 277 105.81 - 112.87: 5951 112.87 - 119.93: 3931 119.93 - 126.99: 5235 126.99 - 134.05: 128 Bond angle restraints: 15522 Sorted by residual: angle pdb=" C VAL A 499 " pdb=" N TRP A 500 " pdb=" CA TRP A 500 " ideal model delta sigma weight residual 121.54 130.30 -8.76 1.91e+00 2.74e-01 2.10e+01 angle pdb=" C VAL B 499 " pdb=" N TRP B 500 " pdb=" CA TRP B 500 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 angle pdb=" N VAL B 191 " pdb=" CA VAL B 191 " pdb=" C VAL B 191 " ideal model delta sigma weight residual 112.29 108.05 4.24 9.40e-01 1.13e+00 2.04e+01 angle pdb=" N VAL A 191 " pdb=" CA VAL A 191 " pdb=" C VAL A 191 " ideal model delta sigma weight residual 112.29 108.10 4.19 9.40e-01 1.13e+00 1.99e+01 angle pdb=" N ILE B 824 " pdb=" CA ILE B 824 " pdb=" C ILE B 824 " ideal model delta sigma weight residual 111.91 109.21 2.70 8.90e-01 1.26e+00 9.17e+00 ... (remaining 15517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 6530 15.26 - 30.53: 172 30.53 - 45.79: 70 45.79 - 61.06: 4 61.06 - 76.32: 4 Dihedral angle restraints: 6780 sinusoidal: 2284 harmonic: 4496 Sorted by residual: dihedral pdb=" CB CYS A 241 " pdb=" SG CYS A 241 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual -86.00 -150.69 64.69 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" CB CYS B 241 " pdb=" SG CYS B 241 " pdb=" SG CYS B 530 " pdb=" CB CYS B 530 " ideal model delta sinusoidal sigma weight residual -86.00 -150.69 64.69 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" CA PHE A 804 " pdb=" C PHE A 804 " pdb=" N SER A 805 " pdb=" CA SER A 805 " ideal model delta harmonic sigma weight residual -180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 6777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1078 0.035 - 0.070: 494 0.070 - 0.105: 184 0.105 - 0.140: 55 0.140 - 0.175: 9 Chirality restraints: 1820 Sorted by residual: chirality pdb=" CB VAL A 610 " pdb=" CA VAL A 610 " pdb=" CG1 VAL A 610 " pdb=" CG2 VAL A 610 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" CB VAL B 610 " pdb=" CA VAL B 610 " pdb=" CG1 VAL B 610 " pdb=" CG2 VAL B 610 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA SER B 654 " pdb=" N SER B 654 " pdb=" C SER B 654 " pdb=" CB SER B 654 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 1817 not shown) Planarity restraints: 1996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 577 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO B 578 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 578 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 578 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 577 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO A 578 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 578 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 578 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 779 " -0.009 2.00e-02 2.50e+03 1.32e-02 3.48e+00 pdb=" CG TYR B 779 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR B 779 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 779 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 779 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 779 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 779 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 779 " 0.002 2.00e-02 2.50e+03 ... (remaining 1993 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3682 2.84 - 3.36: 10215 3.36 - 3.87: 18278 3.87 - 4.39: 19558 4.39 - 4.90: 33371 Nonbonded interactions: 85104 Sorted by model distance: nonbonded pdb=" OH TYR B 223 " pdb=" OD1 ASP B 305 " model vdw 2.328 2.440 nonbonded pdb=" OH TYR A 223 " pdb=" OD1 ASP A 305 " model vdw 2.329 2.440 nonbonded pdb=" NE2 GLN A 163 " pdb=" O LEU A 184 " model vdw 2.334 2.520 nonbonded pdb=" NE2 GLN B 163 " pdb=" O LEU B 184 " model vdw 2.335 2.520 nonbonded pdb=" OG SER B 176 " pdb=" OD1 ASP B 178 " model vdw 2.340 2.440 ... (remaining 85099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.100 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.350 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 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 0.048 11358 Z= 0.234 Angle : 0.699 8.761 15522 Z= 0.397 Chirality : 0.046 0.175 1820 Planarity : 0.006 0.051 1992 Dihedral : 8.654 76.320 3828 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.16), residues: 1536 helix: -2.63 (0.14), residues: 688 sheet: -2.65 (0.36), residues: 162 loop : -2.82 (0.20), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 307 HIS 0.007 0.001 HIS B 218 PHE 0.027 0.002 PHE A 165 TYR 0.032 0.002 TYR B 779 ARG 0.006 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2032 time to fit residues: 36.9229 Evaluate side-chains 68 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.238 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.0870 chunk 116 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 chunk 46 optimal weight: 0.4980 chunk 73 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 139 optimal weight: 20.0000 overall best weight: 2.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 HIS A 364 GLN A 704 GLN B 101 HIS ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS B 364 GLN B 704 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11358 Z= 0.218 Angle : 0.569 11.189 15522 Z= 0.293 Chirality : 0.042 0.146 1820 Planarity : 0.004 0.051 1992 Dihedral : 4.805 37.255 1734 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.78 % Allowed : 5.76 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.20), residues: 1536 helix: -0.69 (0.18), residues: 686 sheet: -2.26 (0.34), residues: 206 loop : -2.13 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 575 HIS 0.003 0.001 HIS B 218 PHE 0.015 0.001 PHE B 165 TYR 0.010 0.001 TYR B 209 ARG 0.002 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 1.333 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 82 average time/residue: 0.1949 time to fit residues: 25.4295 Evaluate side-chains 62 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 1.368 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1018 time to fit residues: 2.1587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 140 optimal weight: 8.9990 chunk 151 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11358 Z= 0.268 Angle : 0.593 8.729 15522 Z= 0.304 Chirality : 0.042 0.161 1820 Planarity : 0.004 0.050 1992 Dihedral : 4.917 45.608 1734 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.88 % Allowed : 5.86 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.21), residues: 1536 helix: 0.10 (0.19), residues: 684 sheet: -1.84 (0.38), residues: 188 loop : -1.64 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 557 HIS 0.005 0.001 HIS B 30 PHE 0.017 0.002 PHE B 165 TYR 0.012 0.001 TYR B 209 ARG 0.003 0.001 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 1.180 Fit side-chains outliers start: 9 outliers final: 0 residues processed: 69 average time/residue: 0.1957 time to fit residues: 21.4066 Evaluate side-chains 62 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 20.0000 chunk 105 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 140 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 133 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11358 Z= 0.220 Angle : 0.558 6.835 15522 Z= 0.283 Chirality : 0.041 0.145 1820 Planarity : 0.004 0.046 1992 Dihedral : 4.893 47.333 1734 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.39 % Allowed : 7.23 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.22), residues: 1536 helix: 0.48 (0.20), residues: 692 sheet: -1.80 (0.38), residues: 188 loop : -1.51 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 557 HIS 0.003 0.001 HIS A 53 PHE 0.015 0.001 PHE B 165 TYR 0.009 0.001 TYR A 340 ARG 0.005 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 1.300 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 67 average time/residue: 0.2016 time to fit residues: 21.4783 Evaluate side-chains 62 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.261 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 110 optimal weight: 0.0170 chunk 61 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 40.0000 chunk 133 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 overall best weight: 6.2030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11358 Z= 0.379 Angle : 0.681 11.723 15522 Z= 0.350 Chirality : 0.044 0.181 1820 Planarity : 0.004 0.047 1992 Dihedral : 5.777 57.966 1734 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.98 % Allowed : 6.93 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.22), residues: 1536 helix: 0.29 (0.19), residues: 696 sheet: -1.99 (0.37), residues: 194 loop : -1.46 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 359 HIS 0.007 0.002 HIS B 30 PHE 0.021 0.002 PHE A 363 TYR 0.016 0.002 TYR A 187 ARG 0.007 0.001 ARG B 465 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 1.292 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 67 average time/residue: 0.1960 time to fit residues: 21.1198 Evaluate side-chains 60 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1051 time to fit residues: 2.4310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 20.0000 chunk 134 optimal weight: 0.0470 chunk 29 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 149 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 50.0000 chunk 78 optimal weight: 3.9990 overall best weight: 1.3680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11358 Z= 0.139 Angle : 0.534 11.882 15522 Z= 0.268 Chirality : 0.041 0.139 1820 Planarity : 0.003 0.038 1992 Dihedral : 4.901 47.015 1734 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.29 % Allowed : 7.91 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.22), residues: 1536 helix: 0.78 (0.20), residues: 698 sheet: -2.02 (0.36), residues: 192 loop : -1.23 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 500 HIS 0.003 0.001 HIS B 391 PHE 0.012 0.001 PHE B 165 TYR 0.010 0.001 TYR A 340 ARG 0.005 0.000 ARG B 465 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 1.292 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 65 average time/residue: 0.2110 time to fit residues: 21.8460 Evaluate side-chains 59 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.244 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 125 optimal weight: 40.0000 chunk 83 optimal weight: 0.0020 chunk 148 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11358 Z= 0.129 Angle : 0.545 12.864 15522 Z= 0.269 Chirality : 0.041 0.143 1820 Planarity : 0.003 0.036 1992 Dihedral : 4.510 42.065 1734 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.59 % Allowed : 8.01 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.22), residues: 1536 helix: 1.05 (0.20), residues: 694 sheet: -1.96 (0.36), residues: 188 loop : -1.13 (0.26), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 557 HIS 0.003 0.001 HIS A 391 PHE 0.010 0.001 PHE B 601 TYR 0.013 0.001 TYR B 249 ARG 0.004 0.000 ARG B 465 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 1.294 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 65 average time/residue: 0.2152 time to fit residues: 22.5059 Evaluate side-chains 59 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 20.0000 chunk 88 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 73 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11358 Z= 0.251 Angle : 0.603 12.856 15522 Z= 0.301 Chirality : 0.042 0.157 1820 Planarity : 0.004 0.035 1992 Dihedral : 4.948 48.652 1734 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.39 % Allowed : 8.59 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.22), residues: 1536 helix: 0.94 (0.20), residues: 696 sheet: -2.07 (0.35), residues: 194 loop : -1.08 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 557 HIS 0.004 0.001 HIS B 30 PHE 0.013 0.001 PHE A 363 TYR 0.014 0.001 TYR A 187 ARG 0.005 0.001 ARG B 465 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 1.220 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 63 average time/residue: 0.1913 time to fit residues: 19.6298 Evaluate side-chains 59 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.317 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 137 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 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 222 ASN ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11358 Z= 0.296 Angle : 0.653 12.707 15522 Z= 0.324 Chirality : 0.043 0.147 1820 Planarity : 0.004 0.036 1992 Dihedral : 5.386 53.961 1734 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.29 % Allowed : 8.89 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1536 helix: 0.75 (0.20), residues: 694 sheet: -2.22 (0.35), residues: 194 loop : -1.20 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 557 HIS 0.005 0.001 HIS A 721 PHE 0.017 0.002 PHE A 363 TYR 0.014 0.001 TYR A 723 ARG 0.004 0.001 ARG B 465 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 1.296 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 59 average time/residue: 0.2005 time to fit residues: 19.2803 Evaluate side-chains 61 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 1.269 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1128 time to fit residues: 2.3219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 20.0000 chunk 89 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11358 Z= 0.197 Angle : 0.596 11.475 15522 Z= 0.293 Chirality : 0.041 0.151 1820 Planarity : 0.004 0.036 1992 Dihedral : 5.050 49.633 1734 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.20 % Allowed : 8.79 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.22), residues: 1536 helix: 0.93 (0.20), residues: 694 sheet: -2.41 (0.33), residues: 212 loop : -1.02 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 557 HIS 0.002 0.001 HIS B 30 PHE 0.013 0.001 PHE B 165 TYR 0.012 0.001 TYR A 187 ARG 0.004 0.000 ARG A 465 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 1.214 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 0.1987 time to fit residues: 19.5281 Evaluate side-chains 60 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 1.308 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1313 time to fit residues: 1.9795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 125 optimal weight: 50.0000 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.060659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.042509 restraints weight = 76368.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.043492 restraints weight = 45486.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.044232 restraints weight = 29780.312| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11358 Z= 0.164 Angle : 0.596 10.929 15522 Z= 0.289 Chirality : 0.041 0.149 1820 Planarity : 0.004 0.035 1992 Dihedral : 4.820 46.473 1734 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.23), residues: 1536 helix: 1.04 (0.20), residues: 694 sheet: -2.39 (0.33), residues: 212 loop : -0.96 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 557 HIS 0.002 0.001 HIS B 391 PHE 0.026 0.001 PHE B 818 TYR 0.010 0.001 TYR A 187 ARG 0.004 0.000 ARG B 465 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1745.68 seconds wall clock time: 32 minutes 49.27 seconds (1969.27 seconds total)