Starting phenix.real_space_refine on Fri Mar 15 08:44:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n52_0346/03_2024/6n52_0346.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n52_0346/03_2024/6n52_0346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n52_0346/03_2024/6n52_0346.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n52_0346/03_2024/6n52_0346.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n52_0346/03_2024/6n52_0346.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n52_0346/03_2024/6n52_0346.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 7096 2.51 5 N 1878 2.21 5 O 2026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11108 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5526 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 740} Chain breaks: 2 Unresolved non-hydrogen bonds: 598 Unresolved non-hydrogen angles: 743 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 6, 'GLU:plan': 20, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 325 Chain: "B" Number of atoms: 5526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5526 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 740} Chain breaks: 2 Unresolved non-hydrogen bonds: 598 Unresolved non-hydrogen angles: 743 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 6, 'GLU:plan': 20, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 325 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.17, per 1000 atoms: 0.56 Number of scatterers: 11108 At special positions: 0 Unit cell: (117.66, 79.5, 183.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 2026 8.00 N 1878 7.00 C 7096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.04 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.03 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 210 " " NAG A 902 " - " ASN A 445 " " NAG B 901 " - " ASN B 210 " " NAG B 902 " - " ASN B 445 " Time building additional restraints: 4.04 Conformation dependent library (CDL) restraints added in 2.3 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: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.945A pdb=" N VAL A 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 81 Processing helix chain 'A' and resid 101 through 122 Processing helix chain 'A' and resid 151 through 163 removed outlier: 4.120A pdb=" N GLN A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN A 160 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 195 through 210 removed outlier: 3.706A pdb=" N VAL A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 236 removed outlier: 3.645A pdb=" N SER A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 227 " --> pdb=" O TYR A 223 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 279 through 294 Processing helix chain 'A' and resid 305 through 308 removed outlier: 3.609A pdb=" N ALA A 308 " --> pdb=" O ASP A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 305 through 308' Processing helix chain 'A' and resid 334 through 343 removed outlier: 3.540A pdb=" N ASP A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 363 removed outlier: 3.729A pdb=" N PHE A 363 " --> pdb=" O TRP A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 419 removed outlier: 3.708A pdb=" N VAL A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 434 through 443 removed outlier: 3.819A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 598 removed outlier: 3.988A pdb=" N ALA A 582 " --> pdb=" O PRO A 578 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA A 583 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 612 removed outlier: 3.689A pdb=" N SER A 612 " --> pdb=" O PRO A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 636 removed outlier: 4.044A pdb=" N THR A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 668 removed outlier: 4.082A pdb=" N GLY A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE A 651 " --> pdb=" O GLN A 647 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY A 652 " --> pdb=" O ARG A 648 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) Proline residue: A 655 - end of helix removed outlier: 3.663A pdb=" N SER A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 662 " --> pdb=" O SER A 658 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 715 removed outlier: 4.243A pdb=" N ALA A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET A 714 " --> pdb=" O ALA A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 761 Proline residue: A 743 - end of helix removed outlier: 3.594A pdb=" N TYR A 746 " --> pdb=" O THR A 742 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 794 removed outlier: 6.264A pdb=" N ALA A 771 " --> pdb=" O ASN A 767 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR A 780 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 783 " --> pdb=" O TYR A 779 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 786 " --> pdb=" O CYS A 782 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL A 789 " --> pdb=" O TRP A 785 " (cutoff:3.500A) Proline residue: A 790 - end of helix Processing helix chain 'A' and resid 799 through 816 removed outlier: 3.757A pdb=" N VAL A 806 " --> pdb=" O MET A 802 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A 807 " --> pdb=" O CYS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 832 removed outlier: 3.698A pdb=" N ARG A 831 " --> pdb=" O LYS A 828 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN A 832 " --> pdb=" O PRO A 829 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 828 through 832' Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.944A pdb=" N VAL B 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 81 Processing helix chain 'B' and resid 101 through 122 Processing helix chain 'B' and resid 151 through 163 removed outlier: 4.119A pdb=" N GLN B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN B 160 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 195 through 210 removed outlier: 3.707A pdb=" N VAL B 206 " --> pdb=" O MET B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 236 removed outlier: 3.644A pdb=" N SER B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 227 " --> pdb=" O TYR B 223 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 279 through 294 Processing helix chain 'B' and resid 305 through 308 removed outlier: 3.609A pdb=" N ALA B 308 " --> pdb=" O ASP B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 305 through 308' Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.541A pdb=" N ASP B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 363 removed outlier: 3.729A pdb=" N PHE B 363 " --> pdb=" O TRP B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 419 removed outlier: 3.707A pdb=" N VAL B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 401 " --> pdb=" O MET B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 434 through 443 removed outlier: 3.818A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 598 removed outlier: 3.988A pdb=" N ALA B 582 " --> pdb=" O PRO B 578 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA B 583 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 removed outlier: 3.689A pdb=" N SER B 612 " --> pdb=" O PRO B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 636 removed outlier: 4.045A pdb=" N THR B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 668 removed outlier: 4.082A pdb=" N GLY B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE B 651 " --> pdb=" O GLN B 647 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 653 " --> pdb=" O ILE B 649 " (cutoff:3.500A) Proline residue: B 655 - end of helix removed outlier: 3.664A pdb=" N SER B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 662 " --> pdb=" O SER B 658 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 715 removed outlier: 4.244A pdb=" N ALA B 697 " --> pdb=" O GLN B 693 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET B 714 " --> pdb=" O ALA B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 761 Proline residue: B 743 - end of helix removed outlier: 3.595A pdb=" N TYR B 746 " --> pdb=" O THR B 742 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 794 removed outlier: 6.265A pdb=" N ALA B 771 " --> pdb=" O ASN B 767 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B 773 " --> pdb=" O ASN B 769 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR B 780 " --> pdb=" O PHE B 776 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B 783 " --> pdb=" O TYR B 779 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 786 " --> pdb=" O CYS B 782 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL B 789 " --> pdb=" O TRP B 785 " (cutoff:3.500A) Proline residue: B 790 - end of helix Processing helix chain 'B' and resid 799 through 816 removed outlier: 3.758A pdb=" N VAL B 806 " --> pdb=" O MET B 802 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER B 807 " --> pdb=" O CYS B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 832 removed outlier: 3.697A pdb=" N ARG B 831 " --> pdb=" O LYS B 828 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN B 832 " --> pdb=" O PRO B 829 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 828 through 832' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.801A pdb=" N GLU A 94 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 41 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE A 36 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY A 145 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ILE A 170 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 242 removed outlier: 9.831A pdb=" N TYR A 246 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ALA A 216 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ILE A 248 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N HIS A 218 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 241 through 242 removed outlier: 6.008A pdb=" N VAL A 273 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 277 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR A 219 " --> pdb=" O PHE A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 329 removed outlier: 3.582A pdb=" N TRP A 487 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ASN A 470 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASN A 483 " --> pdb=" O ASN A 470 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LYS A 472 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N TYR A 481 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 447 removed outlier: 3.686A pdb=" N PHE A 446 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 520 through 521 Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AA9, first strand: chain 'A' and resid 556 through 557 Processing sheet with id=AB1, first strand: chain 'A' and resid 719 through 720 Processing sheet with id=AB2, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.801A pdb=" N GLU B 94 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 41 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE B 36 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY B 145 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ILE B 170 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 241 through 242 removed outlier: 9.831A pdb=" N TYR B 246 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ALA B 216 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N ILE B 248 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N HIS B 218 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 241 through 242 removed outlier: 6.008A pdb=" N VAL B 273 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 277 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR B 219 " --> pdb=" O PHE B 277 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 325 through 329 removed outlier: 3.582A pdb=" N TRP B 487 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASN B 470 " --> pdb=" O ASN B 483 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASN B 483 " --> pdb=" O ASN B 470 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LYS B 472 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR B 481 " --> pdb=" O LYS B 472 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 365 through 366 Processing sheet with id=AB7, first strand: chain 'B' and resid 445 through 447 removed outlier: 3.685A pdb=" N PHE B 446 " --> pdb=" O ILE B 454 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 520 through 521 Processing sheet with id=AB9, first strand: chain 'B' and resid 541 through 543 Processing sheet with id=AC1, first strand: chain 'B' and resid 556 through 557 Processing sheet with id=AC2, first strand: chain 'B' and resid 719 through 720 526 hydrogen bonds defined for protein. 1512 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3598 1.34 - 1.46: 2698 1.46 - 1.58: 4910 1.58 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 11358 Sorted by residual: bond pdb=" C SER A 654 " pdb=" N PRO A 655 " ideal model delta sigma weight residual 1.337 1.365 -0.028 1.24e-02 6.50e+03 4.94e+00 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.84e+00 bond pdb=" C SER B 654 " pdb=" N PRO B 655 " ideal model delta sigma weight residual 1.337 1.364 -0.027 1.24e-02 6.50e+03 4.82e+00 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C1 NAG A 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.01e+00 ... (remaining 11353 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.81: 277 105.81 - 112.87: 5951 112.87 - 119.93: 3931 119.93 - 126.99: 5235 126.99 - 134.05: 128 Bond angle restraints: 15522 Sorted by residual: angle pdb=" C VAL A 499 " pdb=" N TRP A 500 " pdb=" CA TRP A 500 " ideal model delta sigma weight residual 121.54 130.30 -8.76 1.91e+00 2.74e-01 2.10e+01 angle pdb=" C VAL B 499 " pdb=" N TRP B 500 " pdb=" CA TRP B 500 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 angle pdb=" N VAL B 191 " pdb=" CA VAL B 191 " pdb=" C VAL B 191 " ideal model delta sigma weight residual 112.29 108.05 4.24 9.40e-01 1.13e+00 2.04e+01 angle pdb=" N VAL A 191 " pdb=" CA VAL A 191 " pdb=" C VAL A 191 " ideal model delta sigma weight residual 112.29 108.10 4.19 9.40e-01 1.13e+00 1.99e+01 angle pdb=" N ILE B 824 " pdb=" CA ILE B 824 " pdb=" C ILE B 824 " ideal model delta sigma weight residual 111.91 109.21 2.70 8.90e-01 1.26e+00 9.17e+00 ... (remaining 15517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 6530 15.26 - 30.53: 172 30.53 - 45.79: 70 45.79 - 61.06: 4 61.06 - 76.32: 4 Dihedral angle restraints: 6780 sinusoidal: 2284 harmonic: 4496 Sorted by residual: dihedral pdb=" CB CYS A 241 " pdb=" SG CYS A 241 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual -86.00 -150.69 64.69 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" CB CYS B 241 " pdb=" SG CYS B 241 " pdb=" SG CYS B 530 " pdb=" CB CYS B 530 " ideal model delta sinusoidal sigma weight residual -86.00 -150.69 64.69 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" CA PHE A 804 " pdb=" C PHE A 804 " pdb=" N SER A 805 " pdb=" CA SER A 805 " ideal model delta harmonic sigma weight residual -180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 6777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1078 0.035 - 0.070: 494 0.070 - 0.105: 184 0.105 - 0.140: 55 0.140 - 0.175: 9 Chirality restraints: 1820 Sorted by residual: chirality pdb=" CB VAL A 610 " pdb=" CA VAL A 610 " pdb=" CG1 VAL A 610 " pdb=" CG2 VAL A 610 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" CB VAL B 610 " pdb=" CA VAL B 610 " pdb=" CG1 VAL B 610 " pdb=" CG2 VAL B 610 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA SER B 654 " pdb=" N SER B 654 " pdb=" C SER B 654 " pdb=" CB SER B 654 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 1817 not shown) Planarity restraints: 1996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 577 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO B 578 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 578 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 578 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 577 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO A 578 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 578 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 578 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 779 " -0.009 2.00e-02 2.50e+03 1.32e-02 3.48e+00 pdb=" CG TYR B 779 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR B 779 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 779 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 779 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 779 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 779 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 779 " 0.002 2.00e-02 2.50e+03 ... (remaining 1993 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3682 2.84 - 3.36: 10215 3.36 - 3.87: 18278 3.87 - 4.39: 19558 4.39 - 4.90: 33371 Nonbonded interactions: 85104 Sorted by model distance: nonbonded pdb=" OH TYR B 223 " pdb=" OD1 ASP B 305 " model vdw 2.328 2.440 nonbonded pdb=" OH TYR A 223 " pdb=" OD1 ASP A 305 " model vdw 2.329 2.440 nonbonded pdb=" NE2 GLN A 163 " pdb=" O LEU A 184 " model vdw 2.334 2.520 nonbonded pdb=" NE2 GLN B 163 " pdb=" O LEU B 184 " model vdw 2.335 2.520 nonbonded pdb=" OG SER B 176 " pdb=" OD1 ASP B 178 " model vdw 2.340 2.440 ... (remaining 85099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 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: 4.390 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 32.480 Find NCS groups from input model: 0.620 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11358 Z= 0.234 Angle : 0.699 8.761 15522 Z= 0.397 Chirality : 0.046 0.175 1820 Planarity : 0.006 0.051 1992 Dihedral : 8.654 76.320 3828 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.16), residues: 1536 helix: -2.63 (0.14), residues: 688 sheet: -2.65 (0.36), residues: 162 loop : -2.82 (0.20), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 307 HIS 0.007 0.001 HIS B 218 PHE 0.027 0.002 PHE A 165 TYR 0.032 0.002 TYR B 779 ARG 0.006 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.163 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: 0.2027 time to fit residues: 36.7061 Evaluate side-chains 69 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.0870 chunk 116 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 chunk 46 optimal weight: 0.4980 chunk 73 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 139 optimal weight: 20.0000 overall best weight: 2.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 HIS A 364 GLN A 704 GLN B 101 HIS ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS B 364 GLN B 704 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11358 Z= 0.216 Angle : 0.560 11.094 15522 Z= 0.290 Chirality : 0.042 0.145 1820 Planarity : 0.004 0.052 1992 Dihedral : 4.771 37.653 1734 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.78 % Allowed : 5.86 % Favored : 93.36 % 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: -2.29 (0.20), residues: 1536 helix: -0.70 (0.18), residues: 688 sheet: -2.26 (0.34), residues: 206 loop : -2.08 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 575 HIS 0.003 0.001 HIS A 218 PHE 0.015 0.001 PHE B 165 TYR 0.011 0.001 TYR B 209 ARG 0.002 0.000 ARG A 190 *********************** 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 84 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.8930 (ttm) cc_final: 0.8514 (mtt) REVERT: A 778 MET cc_start: 0.8320 (mmm) cc_final: 0.7498 (tmm) REVERT: A 802 MET cc_start: 0.9214 (ttm) cc_final: 0.8849 (ppp) REVERT: B 189 MET cc_start: 0.7878 (mmt) cc_final: 0.6503 (mmt) REVERT: B 414 MET cc_start: 0.8964 (ttm) cc_final: 0.8572 (mtt) REVERT: B 778 MET cc_start: 0.8293 (mmm) cc_final: 0.7823 (tpp) REVERT: B 802 MET cc_start: 0.9246 (ttm) cc_final: 0.8883 (ppp) outliers start: 8 outliers final: 2 residues processed: 84 average time/residue: 0.1906 time to fit residues: 25.5856 Evaluate side-chains 63 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 77 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 151 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11358 Z= 0.415 Angle : 0.721 11.385 15522 Z= 0.370 Chirality : 0.045 0.244 1820 Planarity : 0.005 0.050 1992 Dihedral : 5.653 54.346 1734 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.98 % Allowed : 6.84 % 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: -1.56 (0.21), residues: 1536 helix: -0.12 (0.19), residues: 688 sheet: -1.99 (0.37), residues: 188 loop : -1.65 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 359 HIS 0.007 0.002 HIS B 30 PHE 0.020 0.002 PHE B 165 TYR 0.016 0.002 TYR B 209 ARG 0.004 0.001 ARG B 291 *********************** 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 73 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8559 (mmt) cc_final: 0.8125 (mmm) REVERT: A 469 MET cc_start: 0.8812 (mmm) cc_final: 0.8492 (mmm) REVERT: A 778 MET cc_start: 0.8252 (mmm) cc_final: 0.7506 (tmm) REVERT: A 802 MET cc_start: 0.9239 (ttm) cc_final: 0.8899 (ppp) REVERT: B 72 MET cc_start: 0.9361 (ttp) cc_final: 0.8841 (ppp) REVERT: B 469 MET cc_start: 0.8836 (mmm) cc_final: 0.8516 (mmm) REVERT: B 778 MET cc_start: 0.8254 (mmm) cc_final: 0.7621 (tmm) REVERT: B 802 MET cc_start: 0.9265 (ttm) cc_final: 0.8882 (tmm) outliers start: 10 outliers final: 2 residues processed: 71 average time/residue: 0.1897 time to fit residues: 21.8589 Evaluate side-chains 62 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 286 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 148 optimal weight: 30.0000 chunk 73 optimal weight: 20.0000 chunk 133 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11358 Z= 0.186 Angle : 0.544 10.962 15522 Z= 0.275 Chirality : 0.041 0.236 1820 Planarity : 0.004 0.046 1992 Dihedral : 4.986 48.104 1734 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.49 % Allowed : 7.13 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.22), residues: 1536 helix: 0.44 (0.19), residues: 692 sheet: -1.96 (0.37), residues: 188 loop : -1.45 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 557 HIS 0.002 0.001 HIS A 391 PHE 0.015 0.001 PHE B 165 TYR 0.010 0.001 TYR A 340 ARG 0.003 0.000 ARG A 190 *********************** 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 70 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 1.312 Fit side-chains REVERT: A 72 MET cc_start: 0.9342 (OUTLIER) cc_final: 0.8995 (ppp) REVERT: A 202 MET cc_start: 0.9158 (mmt) cc_final: 0.8895 (mmt) REVERT: A 778 MET cc_start: 0.8271 (mmm) cc_final: 0.7606 (tmm) REVERT: A 802 MET cc_start: 0.9235 (ttm) cc_final: 0.8886 (ppp) REVERT: B 72 MET cc_start: 0.9320 (ttp) cc_final: 0.8894 (ppp) REVERT: B 202 MET cc_start: 0.9164 (mmt) cc_final: 0.8877 (mmt) REVERT: B 778 MET cc_start: 0.8240 (mmm) cc_final: 0.7567 (tmm) REVERT: B 802 MET cc_start: 0.9253 (ttm) cc_final: 0.8894 (ppp) outliers start: 5 outliers final: 2 residues processed: 68 average time/residue: 0.2246 time to fit residues: 23.2258 Evaluate side-chains 65 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 286 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 110 optimal weight: 0.0030 chunk 61 optimal weight: 7.9990 chunk 127 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 37 optimal weight: 20.0000 overall best weight: 2.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11358 Z= 0.183 Angle : 0.536 8.718 15522 Z= 0.270 Chirality : 0.041 0.133 1820 Planarity : 0.003 0.043 1992 Dihedral : 4.773 46.690 1734 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.27 % Allowed : 7.62 % Favored : 91.11 % 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: -0.70 (0.22), residues: 1536 helix: 0.77 (0.20), residues: 692 sheet: -1.95 (0.37), residues: 188 loop : -1.30 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 557 HIS 0.002 0.001 HIS A 53 PHE 0.013 0.001 PHE B 165 TYR 0.008 0.001 TYR A 340 ARG 0.005 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 1.186 Fit side-chains REVERT: A 72 MET cc_start: 0.9362 (OUTLIER) cc_final: 0.8997 (ppp) REVERT: A 202 MET cc_start: 0.9086 (mmt) cc_final: 0.8798 (mmt) REVERT: A 442 MET cc_start: 0.8330 (mmm) cc_final: 0.8119 (mmm) REVERT: A 469 MET cc_start: 0.8774 (mmm) cc_final: 0.8558 (mmm) REVERT: A 494 MET cc_start: 0.7547 (mmm) cc_final: 0.7077 (tpp) REVERT: A 657 MET cc_start: 0.8134 (ptm) cc_final: 0.7922 (ppp) REVERT: A 778 MET cc_start: 0.8260 (mmm) cc_final: 0.7575 (tmm) REVERT: A 802 MET cc_start: 0.9265 (ttm) cc_final: 0.8921 (ppp) REVERT: B 72 MET cc_start: 0.9311 (OUTLIER) cc_final: 0.8880 (ppp) REVERT: B 202 MET cc_start: 0.9092 (mmt) cc_final: 0.8802 (mmt) REVERT: B 494 MET cc_start: 0.7457 (mmm) cc_final: 0.6785 (tpp) REVERT: B 778 MET cc_start: 0.8252 (mmm) cc_final: 0.7604 (tmm) REVERT: B 802 MET cc_start: 0.9278 (ttm) cc_final: 0.8925 (ppp) outliers start: 13 outliers final: 2 residues processed: 71 average time/residue: 0.1812 time to fit residues: 21.0821 Evaluate side-chains 65 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 20.0000 chunk 134 optimal weight: 0.0030 chunk 29 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 50.0000 chunk 78 optimal weight: 3.9990 overall best weight: 4.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11358 Z= 0.264 Angle : 0.575 7.667 15522 Z= 0.295 Chirality : 0.041 0.130 1820 Planarity : 0.004 0.043 1992 Dihedral : 5.120 51.475 1734 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.88 % Allowed : 7.91 % Favored : 91.21 % 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: -0.71 (0.22), residues: 1536 helix: 0.75 (0.20), residues: 696 sheet: -2.05 (0.36), residues: 194 loop : -1.25 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 500 HIS 0.004 0.001 HIS A 30 PHE 0.015 0.001 PHE B 165 TYR 0.009 0.001 TYR A 340 ARG 0.004 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 1.379 Fit side-chains REVERT: A 72 MET cc_start: 0.9384 (OUTLIER) cc_final: 0.9102 (ppp) REVERT: A 202 MET cc_start: 0.9114 (mmt) cc_final: 0.8837 (mmt) REVERT: A 494 MET cc_start: 0.7453 (mmm) cc_final: 0.6900 (tpp) REVERT: A 657 MET cc_start: 0.8180 (ptm) cc_final: 0.7807 (ppp) REVERT: A 778 MET cc_start: 0.8231 (mmm) cc_final: 0.7562 (tmm) REVERT: A 802 MET cc_start: 0.9271 (ttm) cc_final: 0.8924 (ppp) REVERT: A 818 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.8975 (m-80) REVERT: B 72 MET cc_start: 0.9347 (OUTLIER) cc_final: 0.8933 (ppp) REVERT: B 202 MET cc_start: 0.9089 (mmt) cc_final: 0.8809 (mmt) REVERT: B 249 TYR cc_start: 0.8085 (t80) cc_final: 0.7740 (t80) REVERT: B 494 MET cc_start: 0.7425 (mmm) cc_final: 0.6882 (tpp) REVERT: B 778 MET cc_start: 0.8226 (mmm) cc_final: 0.7549 (tmm) REVERT: B 802 MET cc_start: 0.9285 (ttm) cc_final: 0.8928 (ppp) outliers start: 9 outliers final: 2 residues processed: 66 average time/residue: 0.1847 time to fit residues: 20.0047 Evaluate side-chains 64 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 818 PHE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 286 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 125 optimal weight: 50.0000 chunk 83 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 68 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11358 Z= 0.150 Angle : 0.553 12.666 15522 Z= 0.270 Chirality : 0.041 0.152 1820 Planarity : 0.003 0.040 1992 Dihedral : 4.726 46.316 1734 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.49 % Allowed : 8.89 % Favored : 90.62 % 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: -0.47 (0.22), residues: 1536 helix: 1.02 (0.20), residues: 692 sheet: -2.08 (0.35), residues: 192 loop : -1.15 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 500 HIS 0.002 0.001 HIS B 30 PHE 0.012 0.001 PHE A 165 TYR 0.007 0.001 TYR A 341 ARG 0.003 0.000 ARG B 465 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 1.352 Fit side-chains REVERT: A 72 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.9038 (ppp) REVERT: A 202 MET cc_start: 0.9191 (mmt) cc_final: 0.8894 (mmt) REVERT: A 469 MET cc_start: 0.8387 (tpp) cc_final: 0.7649 (tpp) REVERT: A 494 MET cc_start: 0.7306 (mmm) cc_final: 0.6967 (tpp) REVERT: A 657 MET cc_start: 0.8138 (ptm) cc_final: 0.7755 (ppp) REVERT: A 778 MET cc_start: 0.8210 (mmm) cc_final: 0.7554 (tmm) REVERT: A 802 MET cc_start: 0.9268 (ttm) cc_final: 0.8931 (ppp) REVERT: A 818 PHE cc_start: 0.9341 (OUTLIER) cc_final: 0.9005 (m-80) REVERT: B 72 MET cc_start: 0.9330 (OUTLIER) cc_final: 0.8947 (ppp) REVERT: B 202 MET cc_start: 0.9187 (mmt) cc_final: 0.8883 (mmt) REVERT: B 249 TYR cc_start: 0.7910 (t80) cc_final: 0.7633 (t80) REVERT: B 494 MET cc_start: 0.7309 (mmm) cc_final: 0.7022 (tpp) REVERT: B 778 MET cc_start: 0.8188 (mmm) cc_final: 0.7511 (tmm) REVERT: B 802 MET cc_start: 0.9285 (ttm) cc_final: 0.8933 (ppp) outliers start: 5 outliers final: 2 residues processed: 62 average time/residue: 0.2128 time to fit residues: 21.1932 Evaluate side-chains 64 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 1.404 ------------------------------------------------------------------------------- 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 818 PHE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 286 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11358 Z= 0.147 Angle : 0.533 8.787 15522 Z= 0.264 Chirality : 0.041 0.148 1820 Planarity : 0.003 0.038 1992 Dihedral : 4.484 43.623 1734 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.68 % Allowed : 9.18 % Favored : 90.14 % 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: -0.29 (0.22), residues: 1536 helix: 1.16 (0.20), residues: 694 sheet: -2.01 (0.35), residues: 188 loop : -1.06 (0.26), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 500 HIS 0.002 0.001 HIS B 721 PHE 0.011 0.001 PHE B 601 TYR 0.006 0.001 TYR A 340 ARG 0.003 0.000 ARG B 465 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 1.390 Fit side-chains REVERT: A 72 MET cc_start: 0.9359 (OUTLIER) cc_final: 0.9051 (ppp) REVERT: A 202 MET cc_start: 0.9143 (mmt) cc_final: 0.8854 (mmt) REVERT: A 469 MET cc_start: 0.8409 (tpp) cc_final: 0.7758 (tpp) REVERT: A 494 MET cc_start: 0.7393 (mmm) cc_final: 0.7085 (tpp) REVERT: A 778 MET cc_start: 0.8173 (mmm) cc_final: 0.7535 (tmm) REVERT: A 802 MET cc_start: 0.9284 (ttm) cc_final: 0.8957 (ppp) REVERT: A 818 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8940 (m-80) REVERT: B 72 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.8934 (ppp) REVERT: B 202 MET cc_start: 0.9132 (mmt) cc_final: 0.8842 (mmt) REVERT: B 249 TYR cc_start: 0.7923 (t80) cc_final: 0.7637 (t80) REVERT: B 469 MET cc_start: 0.8572 (mmm) cc_final: 0.7879 (tpp) REVERT: B 494 MET cc_start: 0.7303 (mmm) cc_final: 0.7004 (tpp) REVERT: B 778 MET cc_start: 0.8176 (mmm) cc_final: 0.7507 (tmm) REVERT: B 802 MET cc_start: 0.9298 (ttm) cc_final: 0.8963 (ppp) outliers start: 7 outliers final: 3 residues processed: 69 average time/residue: 0.1826 time to fit residues: 20.7176 Evaluate side-chains 66 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 286 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 40.0000 chunk 129 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 chunk 83 optimal weight: 8.9990 chunk 60 optimal weight: 30.0000 chunk 108 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 124 optimal weight: 0.9990 chunk 130 optimal weight: 30.0000 chunk 137 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11358 Z= 0.199 Angle : 0.581 12.417 15522 Z= 0.284 Chirality : 0.041 0.160 1820 Planarity : 0.004 0.037 1992 Dihedral : 4.637 46.315 1734 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.68 % Allowed : 9.57 % 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: -0.37 (0.22), residues: 1536 helix: 1.09 (0.20), residues: 696 sheet: -2.05 (0.35), residues: 190 loop : -1.08 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 557 HIS 0.002 0.001 HIS B 390 PHE 0.011 0.001 PHE B 601 TYR 0.008 0.001 TYR B 187 ARG 0.003 0.000 ARG B 465 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 1.260 Fit side-chains REVERT: A 72 MET cc_start: 0.9388 (OUTLIER) cc_final: 0.9066 (ppp) REVERT: A 202 MET cc_start: 0.9184 (mmt) cc_final: 0.8865 (mmt) REVERT: A 469 MET cc_start: 0.8403 (tpp) cc_final: 0.7784 (tpp) REVERT: A 494 MET cc_start: 0.7499 (mmm) cc_final: 0.7202 (tpp) REVERT: A 778 MET cc_start: 0.8158 (mmm) cc_final: 0.7402 (tpp) REVERT: A 802 MET cc_start: 0.9294 (ttm) cc_final: 0.8933 (tmm) REVERT: A 818 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.9003 (m-80) REVERT: B 72 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.8964 (ppp) REVERT: B 202 MET cc_start: 0.9147 (mmt) cc_final: 0.8816 (mmt) REVERT: B 249 TYR cc_start: 0.7994 (t80) cc_final: 0.7715 (t80) REVERT: B 469 MET cc_start: 0.8691 (mmm) cc_final: 0.7936 (tpp) REVERT: B 494 MET cc_start: 0.7403 (mmm) cc_final: 0.7144 (tpp) REVERT: B 720 MET cc_start: 0.9359 (tmm) cc_final: 0.8710 (pmm) REVERT: B 778 MET cc_start: 0.8165 (mmm) cc_final: 0.7380 (tpp) REVERT: B 802 MET cc_start: 0.9321 (ttm) cc_final: 0.8956 (tmm) REVERT: B 818 PHE cc_start: 0.9355 (OUTLIER) cc_final: 0.8964 (m-80) outliers start: 7 outliers final: 3 residues processed: 63 average time/residue: 0.1879 time to fit residues: 19.2422 Evaluate side-chains 65 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 286 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 69 optimal weight: 30.0000 chunk 101 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 30.0000 chunk 97 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11358 Z= 0.163 Angle : 0.547 9.986 15522 Z= 0.270 Chirality : 0.041 0.164 1820 Planarity : 0.003 0.036 1992 Dihedral : 4.483 43.892 1734 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.88 % Allowed : 9.28 % 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: -0.28 (0.23), residues: 1536 helix: 1.17 (0.20), residues: 696 sheet: -1.97 (0.35), residues: 192 loop : -1.07 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 500 HIS 0.002 0.001 HIS A 74 PHE 0.011 0.001 PHE B 601 TYR 0.007 0.001 TYR A 340 ARG 0.003 0.000 ARG A 465 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 1.365 Fit side-chains REVERT: A 72 MET cc_start: 0.9373 (OUTLIER) cc_final: 0.9074 (ppp) REVERT: A 202 MET cc_start: 0.9128 (mmt) cc_final: 0.8838 (mmt) REVERT: A 469 MET cc_start: 0.8408 (tpp) cc_final: 0.7775 (tpp) REVERT: A 494 MET cc_start: 0.7417 (mmm) cc_final: 0.7137 (tpp) REVERT: A 778 MET cc_start: 0.8152 (mmm) cc_final: 0.7385 (tpp) REVERT: A 802 MET cc_start: 0.9297 (ttm) cc_final: 0.8932 (tmm) REVERT: A 818 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.8913 (m-80) REVERT: B 72 MET cc_start: 0.9352 (OUTLIER) cc_final: 0.8927 (ppp) REVERT: B 202 MET cc_start: 0.9122 (mmt) cc_final: 0.8836 (mmt) REVERT: B 249 TYR cc_start: 0.7923 (t80) cc_final: 0.7665 (t80) REVERT: B 469 MET cc_start: 0.8673 (mmm) cc_final: 0.7945 (tpp) REVERT: B 494 MET cc_start: 0.7288 (mmm) cc_final: 0.7020 (tpp) REVERT: B 720 MET cc_start: 0.9232 (tmm) cc_final: 0.8683 (pmm) REVERT: B 778 MET cc_start: 0.8162 (mmm) cc_final: 0.7362 (tpp) REVERT: B 802 MET cc_start: 0.9317 (ttm) cc_final: 0.8941 (tmm) REVERT: B 818 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8937 (m-80) outliers start: 9 outliers final: 3 residues processed: 67 average time/residue: 0.1861 time to fit residues: 20.2230 Evaluate side-chains 67 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 286 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 51 optimal weight: 30.0000 chunk 125 optimal weight: 50.0000 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.059928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.041426 restraints weight = 75589.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.042383 restraints weight = 44398.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.043025 restraints weight = 30034.412| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11358 Z= 0.235 Angle : 0.603 14.945 15522 Z= 0.297 Chirality : 0.042 0.152 1820 Planarity : 0.004 0.037 1992 Dihedral : 4.759 47.801 1734 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % 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: -0.40 (0.22), residues: 1536 helix: 1.07 (0.20), residues: 694 sheet: -2.13 (0.35), residues: 194 loop : -1.09 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 557 HIS 0.003 0.001 HIS A 53 PHE 0.013 0.001 PHE A 363 TYR 0.011 0.001 TYR B 409 ARG 0.003 0.000 ARG B 465 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1814.75 seconds wall clock time: 33 minutes 45.01 seconds (2025.01 seconds total)