Starting phenix.real_space_refine on Tue Jul 29 10:43:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n52_0346/07_2025/6n52_0346.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n52_0346/07_2025/6n52_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/cci-nas-00/data/ceres_data/6n52_0346/07_2025/6n52_0346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n52_0346/07_2025/6n52_0346.map" model { file = "/net/cci-nas-00/data/ceres_data/6n52_0346/07_2025/6n52_0346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n52_0346/07_2025/6n52_0346.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.26, per 1000 atoms: 0.65 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 - 3.00 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 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: 2.61 Conformation dependent library (CDL) restraints added in 1.6 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: 1.35 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: 4.06 Time building geometry restraints manager: 3.18 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: 0.00 - 1.75: 15063 1.75 - 3.50: 397 3.50 - 5.26: 36 5.26 - 7.01: 16 7.01 - 8.76: 10 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 3.040 nonbonded pdb=" OH TYR A 223 " pdb=" OD1 ASP A 305 " model vdw 2.329 3.040 nonbonded pdb=" NE2 GLN A 163 " pdb=" O LEU A 184 " model vdw 2.334 3.120 nonbonded pdb=" NE2 GLN B 163 " pdb=" O LEU B 184 " model vdw 2.335 3.120 nonbonded pdb=" OG SER B 176 " pdb=" OD1 ASP B 178 " model vdw 2.340 3.040 ... (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 Time spend for trying shortcut: 0.06 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: 1.140 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.360 Find NCS groups from input model: 0.230 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.320 ------------------------------------------------------------------------------- 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 11382 Z= 0.183 Angle : 0.715 10.608 15574 Z= 0.401 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00361 ( 4) link_NAG-ASN : angle 5.49700 ( 12) hydrogen bonds : bond 0.15758 ( 524) hydrogen bonds : angle 6.39049 ( 1512) SS BOND : bond 0.00252 ( 20) SS BOND : angle 0.85633 ( 40) covalent geometry : bond 0.00361 (11358) covalent geometry : angle 0.69852 (15522) *********************** 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 to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 TYR cc_start: 0.8212 (p90) cc_final: 0.7929 (p90) REVERT: A 778 MET cc_start: 0.8348 (mmm) cc_final: 0.7787 (tpp) REVERT: A 802 MET cc_start: 0.9143 (ttm) cc_final: 0.8694 (ppp) REVERT: B 442 MET cc_start: 0.8204 (tpp) cc_final: 0.7986 (tpt) REVERT: B 778 MET cc_start: 0.8299 (mmm) cc_final: 0.7743 (tpp) REVERT: B 802 MET cc_start: 0.9159 (ttm) cc_final: 0.8708 (ppp) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1941 time to fit residues: 35.1769 Evaluate side-chains 69 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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: 0.4980 chunk 116 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 46 optimal weight: 0.0000 chunk 73 optimal weight: 30.0000 chunk 89 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 HIS A 704 GLN B 101 HIS ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS B 704 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.063624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.045008 restraints weight = 76373.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.046083 restraints weight = 44458.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.046851 restraints weight = 29450.925| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11382 Z= 0.115 Angle : 0.548 11.233 15574 Z= 0.279 Chirality : 0.042 0.192 1820 Planarity : 0.004 0.051 1992 Dihedral : 4.590 33.392 1734 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.59 % Allowed : 5.86 % Favored : 93.55 % 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: -2.39 (0.20), residues: 1536 helix: -0.76 (0.18), residues: 690 sheet: -2.42 (0.33), residues: 206 loop : -2.11 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 575 HIS 0.002 0.001 HIS B 218 PHE 0.014 0.001 PHE A 165 TYR 0.007 0.001 TYR A 779 ARG 0.002 0.000 ARG A 291 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 4) link_NAG-ASN : angle 2.97441 ( 12) hydrogen bonds : bond 0.02945 ( 524) hydrogen bonds : angle 4.56086 ( 1512) SS BOND : bond 0.00119 ( 20) SS BOND : angle 0.90985 ( 40) covalent geometry : bond 0.00245 (11358) covalent geometry : angle 0.54098 (15522) *********************** 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 80 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 1.293 Fit side-chains REVERT: A 189 MET cc_start: 0.7458 (mmt) cc_final: 0.5508 (mmt) REVERT: A 778 MET cc_start: 0.8328 (mmm) cc_final: 0.7702 (tpp) REVERT: A 802 MET cc_start: 0.9212 (ttm) cc_final: 0.8752 (ppp) REVERT: B 189 MET cc_start: 0.7622 (mmt) cc_final: 0.6322 (mmt) REVERT: B 414 MET cc_start: 0.8893 (ttm) cc_final: 0.8622 (mtt) REVERT: B 778 MET cc_start: 0.8331 (mmm) cc_final: 0.7904 (tpp) REVERT: B 802 MET cc_start: 0.9215 (ttm) cc_final: 0.8772 (ppp) outliers start: 6 outliers final: 2 residues processed: 80 average time/residue: 0.1988 time to fit residues: 25.4826 Evaluate side-chains 65 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 286 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 1 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 chunk 126 optimal weight: 30.0000 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 48 optimal weight: 30.0000 chunk 14 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN B 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.061111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.042237 restraints weight = 76827.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.043165 restraints weight = 44915.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.043907 restraints weight = 30325.093| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11382 Z= 0.199 Angle : 0.609 9.673 15574 Z= 0.311 Chirality : 0.043 0.216 1820 Planarity : 0.004 0.050 1992 Dihedral : 4.802 41.466 1734 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.27 % Allowed : 5.66 % Favored : 93.07 % 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: -1.48 (0.21), residues: 1536 helix: 0.01 (0.19), residues: 692 sheet: -2.04 (0.37), residues: 188 loop : -1.68 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 487 HIS 0.005 0.002 HIS B 30 PHE 0.018 0.002 PHE B 165 TYR 0.013 0.001 TYR B 209 ARG 0.002 0.000 ARG B 26 Details of bonding type rmsd link_NAG-ASN : bond 0.00118 ( 4) link_NAG-ASN : angle 3.26477 ( 12) hydrogen bonds : bond 0.03073 ( 524) hydrogen bonds : angle 4.53543 ( 1512) SS BOND : bond 0.00164 ( 20) SS BOND : angle 0.79289 ( 40) covalent geometry : bond 0.00418 (11358) covalent geometry : angle 0.60192 (15522) *********************** 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 77 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 1.722 Fit side-chains REVERT: A 72 MET cc_start: 0.9357 (ttp) cc_final: 0.8800 (ppp) REVERT: A 469 MET cc_start: 0.8787 (mmm) cc_final: 0.8274 (mmm) REVERT: A 482 ILE cc_start: 0.9639 (OUTLIER) cc_final: 0.9404 (pt) REVERT: A 778 MET cc_start: 0.8326 (mmm) cc_final: 0.7562 (tmm) REVERT: A 802 MET cc_start: 0.9261 (ttm) cc_final: 0.8903 (ppp) REVERT: B 72 MET cc_start: 0.9377 (ttp) cc_final: 0.8799 (ppp) REVERT: B 469 MET cc_start: 0.8763 (mmm) cc_final: 0.8247 (mmm) REVERT: B 482 ILE cc_start: 0.9637 (OUTLIER) cc_final: 0.9404 (pt) REVERT: B 778 MET cc_start: 0.8269 (mmm) cc_final: 0.7496 (tmm) REVERT: B 802 MET cc_start: 0.9270 (ttm) cc_final: 0.8922 (ppp) outliers start: 13 outliers final: 2 residues processed: 74 average time/residue: 0.1890 time to fit residues: 23.8718 Evaluate side-chains 68 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 482 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 69 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 105 optimal weight: 0.1980 chunk 130 optimal weight: 30.0000 chunk 63 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 55 optimal weight: 40.0000 chunk 49 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 chunk 51 optimal weight: 50.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** 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 = 0.3610 r_free = 0.3610 target = 0.061781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.043066 restraints weight = 74949.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.044053 restraints weight = 45298.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.044780 restraints weight = 30462.781| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11382 Z= 0.108 Angle : 0.526 7.045 15574 Z= 0.263 Chirality : 0.041 0.190 1820 Planarity : 0.003 0.045 1992 Dihedral : 4.415 37.235 1734 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.88 % Allowed : 6.15 % Favored : 92.97 % 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: -0.95 (0.22), residues: 1536 helix: 0.55 (0.19), residues: 694 sheet: -1.93 (0.37), residues: 188 loop : -1.48 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 557 HIS 0.002 0.001 HIS B 74 PHE 0.013 0.001 PHE A 165 TYR 0.008 0.001 TYR B 340 ARG 0.002 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 4) link_NAG-ASN : angle 2.80798 ( 12) hydrogen bonds : bond 0.02561 ( 524) hydrogen bonds : angle 4.31903 ( 1512) SS BOND : bond 0.00090 ( 20) SS BOND : angle 0.64667 ( 40) covalent geometry : bond 0.00235 (11358) covalent geometry : angle 0.51998 (15522) *********************** 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 77 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 1.198 Fit side-chains REVERT: A 72 MET cc_start: 0.9377 (OUTLIER) cc_final: 0.8925 (ppp) REVERT: A 202 MET cc_start: 0.9115 (mmt) cc_final: 0.8826 (mmt) REVERT: A 778 MET cc_start: 0.8299 (mmm) cc_final: 0.7572 (tmm) REVERT: A 802 MET cc_start: 0.9260 (ttm) cc_final: 0.8906 (ppp) REVERT: B 72 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.8902 (ppp) REVERT: B 202 MET cc_start: 0.9073 (mmt) cc_final: 0.8782 (mmt) REVERT: B 778 MET cc_start: 0.8243 (mmm) cc_final: 0.7557 (tmm) REVERT: B 802 MET cc_start: 0.9270 (ttm) cc_final: 0.8923 (ppp) outliers start: 9 outliers final: 2 residues processed: 74 average time/residue: 0.1754 time to fit residues: 21.1378 Evaluate side-chains 66 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 286 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 54 optimal weight: 8.9990 chunk 110 optimal weight: 0.1980 chunk 61 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 overall best weight: 5.6388 ------------------------------------------------------------------------------- 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 163 GLN ** B 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.059061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.040471 restraints weight = 75350.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.041432 restraints weight = 44163.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.042095 restraints weight = 30081.118| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11382 Z= 0.261 Angle : 0.673 12.931 15574 Z= 0.343 Chirality : 0.043 0.148 1820 Planarity : 0.004 0.045 1992 Dihedral : 5.161 44.755 1734 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.17 % Allowed : 6.64 % Favored : 92.19 % 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: -1.07 (0.22), residues: 1536 helix: 0.35 (0.19), residues: 712 sheet: -2.05 (0.35), residues: 192 loop : -1.41 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 359 HIS 0.005 0.002 HIS A 53 PHE 0.019 0.002 PHE A 363 TYR 0.012 0.002 TYR B 340 ARG 0.002 0.001 ARG B 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 4) link_NAG-ASN : angle 3.42678 ( 12) hydrogen bonds : bond 0.03241 ( 524) hydrogen bonds : angle 4.92516 ( 1512) SS BOND : bond 0.00214 ( 20) SS BOND : angle 0.68539 ( 40) covalent geometry : bond 0.00542 (11358) covalent geometry : angle 0.66669 (15522) *********************** 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 73 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 1.253 Fit side-chains REVERT: A 72 MET cc_start: 0.9380 (ttp) cc_final: 0.8964 (ppp) REVERT: A 202 MET cc_start: 0.9138 (mmt) cc_final: 0.8849 (mmt) REVERT: A 249 TYR cc_start: 0.8129 (t80) cc_final: 0.7768 (t80) REVERT: A 494 MET cc_start: 0.7566 (mmm) cc_final: 0.6865 (tpp) REVERT: A 778 MET cc_start: 0.8227 (mmm) cc_final: 0.7558 (tmm) REVERT: A 802 MET cc_start: 0.9303 (ttm) cc_final: 0.8932 (tmm) REVERT: B 72 MET cc_start: 0.9358 (ttp) cc_final: 0.9048 (ppp) REVERT: B 202 MET cc_start: 0.9096 (mmt) cc_final: 0.8806 (mmt) REVERT: B 249 TYR cc_start: 0.8102 (t80) cc_final: 0.7767 (t80) REVERT: B 469 MET cc_start: 0.8790 (mmm) cc_final: 0.8517 (tpp) REVERT: B 494 MET cc_start: 0.7547 (mmm) cc_final: 0.6859 (tpp) REVERT: B 778 MET cc_start: 0.8184 (mmm) cc_final: 0.7502 (tmm) REVERT: B 802 MET cc_start: 0.9311 (ttm) cc_final: 0.8943 (tmm) outliers start: 12 outliers final: 4 residues processed: 72 average time/residue: 0.1894 time to fit residues: 22.3095 Evaluate side-chains 64 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 744 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 105 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 133 optimal weight: 30.0000 chunk 1 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 129 optimal weight: 30.0000 chunk 148 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 64 optimal weight: 40.0000 chunk 99 optimal weight: 20.0000 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 74 HIS ** 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 = 0.3514 r_free = 0.3514 target = 0.058517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.040035 restraints weight = 76342.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.041008 restraints weight = 44627.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.041671 restraints weight = 30155.040| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11382 Z= 0.257 Angle : 0.658 8.388 15574 Z= 0.337 Chirality : 0.043 0.142 1820 Planarity : 0.004 0.043 1992 Dihedral : 5.153 41.274 1734 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.78 % Allowed : 8.20 % 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: -1.14 (0.22), residues: 1536 helix: 0.30 (0.19), residues: 712 sheet: -2.26 (0.35), residues: 194 loop : -1.39 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 557 HIS 0.005 0.002 HIS A 30 PHE 0.019 0.002 PHE A 165 TYR 0.015 0.001 TYR B 340 ARG 0.004 0.001 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 4) link_NAG-ASN : angle 3.48087 ( 12) hydrogen bonds : bond 0.03050 ( 524) hydrogen bonds : angle 4.95616 ( 1512) SS BOND : bond 0.00246 ( 20) SS BOND : angle 0.57738 ( 40) covalent geometry : bond 0.00539 (11358) covalent geometry : angle 0.65151 (15522) *********************** 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 66 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 1.295 Fit side-chains REVERT: A 72 MET cc_start: 0.9327 (ttp) cc_final: 0.8956 (ppp) REVERT: A 202 MET cc_start: 0.9181 (mmt) cc_final: 0.8904 (mmt) REVERT: A 249 TYR cc_start: 0.8192 (t80) cc_final: 0.7741 (t80) REVERT: A 494 MET cc_start: 0.7614 (mmm) cc_final: 0.7149 (tpp) REVERT: A 778 MET cc_start: 0.8241 (mmm) cc_final: 0.7598 (tmm) REVERT: A 802 MET cc_start: 0.9303 (ttm) cc_final: 0.8927 (tmm) REVERT: A 818 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.8905 (m-80) REVERT: B 72 MET cc_start: 0.9323 (ttp) cc_final: 0.8927 (ppp) REVERT: B 202 MET cc_start: 0.9152 (mmt) cc_final: 0.8869 (mmt) REVERT: B 249 TYR cc_start: 0.8162 (t80) cc_final: 0.7740 (t80) REVERT: B 494 MET cc_start: 0.7612 (mmm) cc_final: 0.7159 (tpp) REVERT: B 778 MET cc_start: 0.8194 (mmm) cc_final: 0.7555 (tmm) REVERT: B 802 MET cc_start: 0.9309 (ttm) cc_final: 0.8932 (tmm) outliers start: 8 outliers final: 7 residues processed: 66 average time/residue: 0.1909 time to fit residues: 20.4084 Evaluate side-chains 63 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 818 PHE Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 744 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 147 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.059009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.040357 restraints weight = 74793.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.041372 restraints weight = 42509.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.042065 restraints weight = 29296.394| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11382 Z= 0.213 Angle : 0.635 13.764 15574 Z= 0.318 Chirality : 0.043 0.149 1820 Planarity : 0.004 0.041 1992 Dihedral : 5.090 42.501 1734 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.07 % Allowed : 8.40 % Favored : 90.53 % 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: -0.99 (0.22), residues: 1536 helix: 0.48 (0.19), residues: 712 sheet: -2.28 (0.34), residues: 192 loop : -1.36 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 557 HIS 0.005 0.001 HIS A 30 PHE 0.016 0.002 PHE A 165 TYR 0.013 0.001 TYR A 746 ARG 0.002 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 4) link_NAG-ASN : angle 3.42874 ( 12) hydrogen bonds : bond 0.02975 ( 524) hydrogen bonds : angle 4.86883 ( 1512) SS BOND : bond 0.00185 ( 20) SS BOND : angle 0.54625 ( 40) covalent geometry : bond 0.00448 (11358) covalent geometry : angle 0.62796 (15522) *********************** 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 69 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 1.411 Fit side-chains REVERT: A 72 MET cc_start: 0.9404 (ttp) cc_final: 0.8998 (ppp) REVERT: A 202 MET cc_start: 0.9232 (mmt) cc_final: 0.9002 (mmt) REVERT: A 249 TYR cc_start: 0.8223 (t80) cc_final: 0.7775 (t80) REVERT: A 494 MET cc_start: 0.7522 (mmm) cc_final: 0.7234 (tpp) REVERT: A 778 MET cc_start: 0.8166 (mmm) cc_final: 0.7574 (tmm) REVERT: A 802 MET cc_start: 0.9313 (ttm) cc_final: 0.8951 (tmm) REVERT: A 818 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8876 (m-80) REVERT: B 72 MET cc_start: 0.9411 (OUTLIER) cc_final: 0.8972 (ppp) REVERT: B 202 MET cc_start: 0.9183 (mmt) cc_final: 0.8900 (mmt) REVERT: B 234 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8463 (mtm) REVERT: B 249 TYR cc_start: 0.8211 (t80) cc_final: 0.7781 (t80) REVERT: B 494 MET cc_start: 0.7567 (mmm) cc_final: 0.7277 (tpp) REVERT: B 778 MET cc_start: 0.8177 (mmm) cc_final: 0.7569 (tmm) REVERT: B 802 MET cc_start: 0.9316 (ttm) cc_final: 0.8943 (tmm) REVERT: B 818 PHE cc_start: 0.9297 (OUTLIER) cc_final: 0.8981 (m-80) outliers start: 11 outliers final: 6 residues processed: 67 average time/residue: 0.2307 time to fit residues: 23.8154 Evaluate side-chains 66 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 818 PHE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 818 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 4 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 33 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 40.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.059562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.040905 restraints weight = 73676.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.041882 restraints weight = 42880.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.042528 restraints weight = 28924.827| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11382 Z= 0.144 Angle : 0.568 6.990 15574 Z= 0.287 Chirality : 0.041 0.137 1820 Planarity : 0.004 0.038 1992 Dihedral : 4.755 38.819 1734 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.88 % Allowed : 8.89 % Favored : 90.23 % 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: -0.68 (0.22), residues: 1536 helix: 0.82 (0.20), residues: 708 sheet: -2.41 (0.32), residues: 210 loop : -1.15 (0.27), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 557 HIS 0.003 0.001 HIS A 30 PHE 0.013 0.001 PHE B 165 TYR 0.011 0.001 TYR B 340 ARG 0.008 0.000 ARG A 465 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 4) link_NAG-ASN : angle 3.03244 ( 12) hydrogen bonds : bond 0.02595 ( 524) hydrogen bonds : angle 4.65197 ( 1512) SS BOND : bond 0.00128 ( 20) SS BOND : angle 0.48972 ( 40) covalent geometry : bond 0.00308 (11358) covalent geometry : angle 0.56213 (15522) *********************** 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 68 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 1.338 Fit side-chains REVERT: A 72 MET cc_start: 0.9381 (ttp) cc_final: 0.8958 (ppp) REVERT: A 202 MET cc_start: 0.9209 (mmt) cc_final: 0.8930 (mmt) REVERT: A 249 TYR cc_start: 0.8189 (t80) cc_final: 0.7824 (t80) REVERT: A 494 MET cc_start: 0.7434 (mmm) cc_final: 0.7179 (tpp) REVERT: A 720 MET cc_start: 0.9172 (ppp) cc_final: 0.8460 (pmm) REVERT: A 778 MET cc_start: 0.8174 (mmm) cc_final: 0.7584 (tmm) REVERT: A 802 MET cc_start: 0.9317 (ttm) cc_final: 0.8938 (tmm) REVERT: A 818 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8889 (m-80) REVERT: B 72 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.8978 (ppp) REVERT: B 202 MET cc_start: 0.9200 (mmt) cc_final: 0.8922 (mmt) REVERT: B 249 TYR cc_start: 0.8159 (t80) cc_final: 0.7810 (t80) REVERT: B 494 MET cc_start: 0.7438 (mmm) cc_final: 0.7182 (tpp) REVERT: B 720 MET cc_start: 0.9157 (ppp) cc_final: 0.8453 (pmm) REVERT: B 778 MET cc_start: 0.8168 (mmm) cc_final: 0.7558 (tmm) REVERT: B 802 MET cc_start: 0.9318 (ttm) cc_final: 0.8932 (tmm) REVERT: B 818 PHE cc_start: 0.9311 (OUTLIER) cc_final: 0.8906 (m-80) outliers start: 9 outliers final: 3 residues processed: 66 average time/residue: 0.1859 time to fit residues: 19.8665 Evaluate side-chains 64 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 818 PHE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 818 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 11 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 142 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.058663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.039932 restraints weight = 74294.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.040861 restraints weight = 44923.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.041576 restraints weight = 30172.489| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11382 Z= 0.245 Angle : 0.688 11.886 15574 Z= 0.342 Chirality : 0.044 0.185 1820 Planarity : 0.004 0.038 1992 Dihedral : 5.117 42.606 1734 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.88 % Allowed : 8.89 % Favored : 90.23 % 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: -0.86 (0.22), residues: 1536 helix: 0.60 (0.19), residues: 712 sheet: -2.17 (0.35), residues: 192 loop : -1.34 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 359 HIS 0.005 0.002 HIS A 30 PHE 0.016 0.002 PHE A 363 TYR 0.011 0.001 TYR B 340 ARG 0.006 0.001 ARG B 465 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 4) link_NAG-ASN : angle 3.35654 ( 12) hydrogen bonds : bond 0.03058 ( 524) hydrogen bonds : angle 5.02537 ( 1512) SS BOND : bond 0.00205 ( 20) SS BOND : angle 0.55385 ( 40) covalent geometry : bond 0.00514 (11358) covalent geometry : angle 0.68215 (15522) *********************** 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 65 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 1.370 Fit side-chains REVERT: A 202 MET cc_start: 0.9164 (mmt) cc_final: 0.8916 (mmt) REVERT: A 249 TYR cc_start: 0.8302 (t80) cc_final: 0.7792 (t80) REVERT: A 720 MET cc_start: 0.9087 (ppp) cc_final: 0.8181 (mpp) REVERT: A 778 MET cc_start: 0.8165 (mmm) cc_final: 0.7307 (tpp) REVERT: A 802 MET cc_start: 0.9382 (ttm) cc_final: 0.9038 (tmm) REVERT: A 818 PHE cc_start: 0.9327 (OUTLIER) cc_final: 0.8908 (m-80) REVERT: B 72 MET cc_start: 0.9389 (OUTLIER) cc_final: 0.9012 (ppp) REVERT: B 202 MET cc_start: 0.9179 (mmt) cc_final: 0.8930 (mmt) REVERT: B 249 TYR cc_start: 0.8261 (t80) cc_final: 0.7754 (t80) REVERT: B 720 MET cc_start: 0.9072 (ppp) cc_final: 0.8173 (mpp) REVERT: B 778 MET cc_start: 0.8175 (mmm) cc_final: 0.7319 (tpp) REVERT: B 802 MET cc_start: 0.9376 (ttm) cc_final: 0.9030 (tmm) REVERT: B 818 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.8901 (m-80) outliers start: 9 outliers final: 6 residues processed: 64 average time/residue: 0.1934 time to fit residues: 20.3004 Evaluate side-chains 65 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 818 PHE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 818 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 43 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 125 optimal weight: 50.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.059811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.041121 restraints weight = 74534.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.042135 restraints weight = 43337.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.042817 restraints weight = 29489.326| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11382 Z= 0.122 Angle : 0.602 10.463 15574 Z= 0.295 Chirality : 0.042 0.187 1820 Planarity : 0.004 0.036 1992 Dihedral : 4.656 37.406 1734 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.78 % Allowed : 9.38 % Favored : 89.84 % 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: -0.54 (0.22), residues: 1536 helix: 1.09 (0.20), residues: 694 sheet: -2.30 (0.34), residues: 210 loop : -1.24 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 557 HIS 0.003 0.001 HIS B 74 PHE 0.013 0.001 PHE B 165 TYR 0.011 0.001 TYR B 340 ARG 0.005 0.000 ARG A 465 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 4) link_NAG-ASN : angle 2.94837 ( 12) hydrogen bonds : bond 0.02625 ( 524) hydrogen bonds : angle 4.65217 ( 1512) SS BOND : bond 0.00114 ( 20) SS BOND : angle 0.47811 ( 40) covalent geometry : bond 0.00268 (11358) covalent geometry : angle 0.59645 (15522) ********************** 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 69 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 1.223 Fit side-chains REVERT: A 72 MET cc_start: 0.9428 (OUTLIER) cc_final: 0.9005 (ppp) REVERT: A 202 MET cc_start: 0.9193 (mmt) cc_final: 0.8968 (mmt) REVERT: A 249 TYR cc_start: 0.8254 (t80) cc_final: 0.7886 (t80) REVERT: A 720 MET cc_start: 0.9114 (ppp) cc_final: 0.8433 (mpp) REVERT: A 778 MET cc_start: 0.8098 (mmm) cc_final: 0.7273 (tpp) REVERT: A 802 MET cc_start: 0.9365 (ttm) cc_final: 0.9042 (tmm) REVERT: A 818 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.8868 (m-80) REVERT: B 72 MET cc_start: 0.9405 (OUTLIER) cc_final: 0.8978 (ppp) REVERT: B 202 MET cc_start: 0.9239 (mmt) cc_final: 0.8958 (mmt) REVERT: B 249 TYR cc_start: 0.8275 (t80) cc_final: 0.7904 (t80) REVERT: B 720 MET cc_start: 0.9079 (ppp) cc_final: 0.8417 (mpp) REVERT: B 778 MET cc_start: 0.8085 (mmm) cc_final: 0.7260 (tpp) REVERT: B 802 MET cc_start: 0.9354 (ttm) cc_final: 0.9032 (tmm) REVERT: B 818 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8874 (m-80) outliers start: 8 outliers final: 4 residues processed: 67 average time/residue: 0.1841 time to fit residues: 20.3145 Evaluate side-chains 68 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 818 PHE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 818 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 85 optimal weight: 0.9980 chunk 146 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 27 optimal weight: 0.0010 chunk 20 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 overall best weight: 4.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.058929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.040176 restraints weight = 73409.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.041117 restraints weight = 44324.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.041668 restraints weight = 29823.679| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11382 Z= 0.206 Angle : 0.656 14.396 15574 Z= 0.325 Chirality : 0.043 0.150 1820 Planarity : 0.004 0.037 1992 Dihedral : 4.912 41.200 1734 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.07 % Allowed : 9.18 % Favored : 89.75 % 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: 0.94 (0.20), residues: 694 sheet: -2.16 (0.35), residues: 192 loop : -1.36 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 557 HIS 0.004 0.001 HIS B 390 PHE 0.014 0.002 PHE B 165 TYR 0.010 0.001 TYR B 340 ARG 0.005 0.000 ARG A 465 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 4) link_NAG-ASN : angle 3.14946 ( 12) hydrogen bonds : bond 0.02896 ( 524) hydrogen bonds : angle 4.87565 ( 1512) SS BOND : bond 0.00175 ( 20) SS BOND : angle 0.50862 ( 40) covalent geometry : bond 0.00438 (11358) covalent geometry : angle 0.65088 (15522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3584.65 seconds wall clock time: 63 minutes 20.36 seconds (3800.36 seconds total)