Starting phenix.real_space_refine on Sat Jul 20 09:45:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcw_37112/07_2024/8kcw_37112_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcw_37112/07_2024/8kcw_37112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcw_37112/07_2024/8kcw_37112.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcw_37112/07_2024/8kcw_37112.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcw_37112/07_2024/8kcw_37112_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcw_37112/07_2024/8kcw_37112_neut.cif" } resolution = 2.77 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 58 5.16 5 C 6934 2.51 5 N 1620 2.21 5 O 1870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 133": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C GLU 232": "OE1" <-> "OE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "C ARG 820": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10484 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5051 Classifications: {'peptide': 626} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 601} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5051 Classifications: {'peptide': 626} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 601} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" 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: "J" 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" 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: "P" 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: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' ZN': 1, 'CLR': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' ZN': 1, 'CLR': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.19, per 1000 atoms: 0.59 Number of scatterers: 10484 At special positions: 0 Unit cell: (93.375, 85.905, 133.215, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 58 16.00 O 1870 8.00 N 1620 7.00 C 6934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 782 " distance=2.03 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 222 " distance=2.03 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 479 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 782 " 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG G 1 " - " ASN A 83 " " NAG H 1 " - " ASN A 136 " " NAG I 1 " - " ASN A 67 " " NAG J 1 " - " ASN A 57 " " NAG M 1 " - " ASN C 83 " " NAG N 1 " - " ASN C 136 " " NAG O 1 " - " ASN C 67 " " NAG P 1 " - " ASN C 57 " Time building additional restraints: 4.17 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 791 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 795 " pdb=" ZN C 901 " pdb="ZN ZN C 901 " - pdb=" NE2 HIS C 791 " pdb="ZN ZN C 901 " - pdb=" NE2 HIS C 563 " pdb="ZN ZN C 901 " - pdb=" NE2 HIS C 795 " 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 48.4% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 302 through 316 removed outlier: 3.790A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 332 removed outlier: 3.922A pdb=" N VAL A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 331 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 473 removed outlier: 3.649A pdb=" N PHE A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) Proline residue: A 458 - end of helix removed outlier: 3.918A pdb=" N ILE A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 471 " --> pdb=" O GLN A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 486 removed outlier: 4.078A pdb=" N ALA A 486 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 500 removed outlier: 3.812A pdb=" N ILE A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 527 removed outlier: 3.951A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 563 removed outlier: 3.620A pdb=" N TYR A 546 " --> pdb=" O PHE A 542 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 575 removed outlier: 3.703A pdb=" N ASP A 574 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 592 removed outlier: 4.132A pdb=" N MET A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 620 removed outlier: 3.569A pdb=" N TYR A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 615 " --> pdb=" O VAL A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 648 removed outlier: 3.538A pdb=" N TRP A 629 " --> pdb=" O ASP A 625 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE A 631 " --> pdb=" O TRP A 627 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 640 " --> pdb=" O HIS A 636 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 705 removed outlier: 3.536A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 688 " --> pdb=" O MET A 684 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 735 removed outlier: 3.520A pdb=" N LEU A 714 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 763 removed outlier: 3.716A pdb=" N PHE A 762 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 763 " --> pdb=" O TYR A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 776 Processing helix chain 'A' and resid 777 through 779 No H-bonds generated for 'chain 'A' and resid 777 through 779' Processing helix chain 'A' and resid 789 through 812 removed outlier: 3.868A pdb=" N ALA A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 800 " --> pdb=" O PHE A 796 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 809 " --> pdb=" O SER A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 815 No H-bonds generated for 'chain 'A' and resid 813 through 815' Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 302 through 316 removed outlier: 3.790A pdb=" N TYR C 306 " --> pdb=" O LYS C 302 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 310 " --> pdb=" O TYR C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 332 removed outlier: 3.922A pdb=" N VAL C 327 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS C 331 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR C 332 " --> pdb=" O GLY C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 473 removed outlier: 3.649A pdb=" N PHE C 454 " --> pdb=" O THR C 450 " (cutoff:3.500A) Proline residue: C 458 - end of helix removed outlier: 3.918A pdb=" N ILE C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR C 465 " --> pdb=" O GLN C 461 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR C 468 " --> pdb=" O ILE C 464 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN C 471 " --> pdb=" O GLN C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 removed outlier: 4.078A pdb=" N ALA C 486 " --> pdb=" O PHE C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 500 removed outlier: 3.812A pdb=" N ILE C 498 " --> pdb=" O ALA C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 527 removed outlier: 3.951A pdb=" N VAL C 505 " --> pdb=" O ASN C 501 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 509 " --> pdb=" O VAL C 505 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 512 " --> pdb=" O GLY C 508 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS C 522 " --> pdb=" O ARG C 518 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU C 527 " --> pdb=" O ARG C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 563 removed outlier: 3.620A pdb=" N TYR C 546 " --> pdb=" O PHE C 542 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY C 556 " --> pdb=" O LEU C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 575 removed outlier: 3.703A pdb=" N ASP C 574 " --> pdb=" O PHE C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 592 removed outlier: 4.132A pdb=" N MET C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 620 removed outlier: 3.569A pdb=" N TYR C 605 " --> pdb=" O ALA C 601 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 615 " --> pdb=" O VAL C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 648 removed outlier: 3.538A pdb=" N TRP C 629 " --> pdb=" O ASP C 625 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE C 631 " --> pdb=" O TRP C 627 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER C 640 " --> pdb=" O HIS C 636 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR C 645 " --> pdb=" O LEU C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 705 removed outlier: 3.536A pdb=" N LEU C 686 " --> pdb=" O ASP C 682 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 688 " --> pdb=" O MET C 684 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN C 691 " --> pdb=" O LEU C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 735 removed outlier: 3.520A pdb=" N LEU C 714 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA C 726 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 729 " --> pdb=" O LEU C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 763 removed outlier: 3.716A pdb=" N PHE C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN C 763 " --> pdb=" O TYR C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 776 Processing helix chain 'C' and resid 777 through 779 No H-bonds generated for 'chain 'C' and resid 777 through 779' Processing helix chain 'C' and resid 789 through 812 removed outlier: 3.868A pdb=" N ALA C 799 " --> pdb=" O HIS C 795 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 800 " --> pdb=" O PHE C 796 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 809 " --> pdb=" O SER C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 815 No H-bonds generated for 'chain 'C' and resid 813 through 815' Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 56 removed outlier: 4.656A pdb=" N ALA A 77 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 114 removed outlier: 3.901A pdb=" N ARG A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 171 removed outlier: 4.877A pdb=" N LYS A 192 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 177 through 181 Processing sheet with id=AA6, first strand: chain 'C' and resid 51 through 56 removed outlier: 4.656A pdb=" N ALA C 77 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 62 through 70 Processing sheet with id=AA8, first strand: chain 'C' and resid 110 through 114 removed outlier: 3.901A pdb=" N ARG C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 170 through 171 removed outlier: 4.877A pdb=" N LYS C 192 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 177 through 181 538 hydrogen bonds defined for protein. 1536 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: 3.19 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3098 1.34 - 1.46: 2768 1.46 - 1.58: 4814 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 10770 Sorted by residual: bond pdb=" N ILE A 449 " pdb=" CA ILE A 449 " ideal model delta sigma weight residual 1.460 1.502 -0.042 1.21e-02 6.83e+03 1.21e+01 bond pdb=" N ILE C 449 " pdb=" CA ILE C 449 " ideal model delta sigma weight residual 1.460 1.502 -0.042 1.21e-02 6.83e+03 1.21e+01 bond pdb=" N ASP C 625 " pdb=" CA ASP C 625 " ideal model delta sigma weight residual 1.454 1.490 -0.037 1.18e-02 7.18e+03 9.62e+00 bond pdb=" N ASP A 625 " pdb=" CA ASP A 625 " ideal model delta sigma weight residual 1.454 1.490 -0.037 1.18e-02 7.18e+03 9.62e+00 bond pdb=" N ILE C 448 " pdb=" CA ILE C 448 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.33e-02 5.65e+03 8.11e+00 ... (remaining 10765 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.21: 262 106.21 - 113.21: 5882 113.21 - 120.22: 4148 120.22 - 127.23: 4288 127.23 - 134.24: 104 Bond angle restraints: 14684 Sorted by residual: angle pdb=" N GLN A 646 " pdb=" CA GLN A 646 " pdb=" C GLN A 646 " ideal model delta sigma weight residual 111.36 107.03 4.33 1.09e+00 8.42e-01 1.57e+01 angle pdb=" N GLN C 646 " pdb=" CA GLN C 646 " pdb=" C GLN C 646 " ideal model delta sigma weight residual 111.36 107.03 4.33 1.09e+00 8.42e-01 1.57e+01 angle pdb=" CB GLN A 646 " pdb=" CG GLN A 646 " pdb=" CD GLN A 646 " ideal model delta sigma weight residual 112.60 119.09 -6.49 1.70e+00 3.46e-01 1.46e+01 angle pdb=" CB GLN C 646 " pdb=" CG GLN C 646 " pdb=" CD GLN C 646 " ideal model delta sigma weight residual 112.60 119.09 -6.49 1.70e+00 3.46e-01 1.46e+01 angle pdb=" CA ASN C 624 " pdb=" C ASN C 624 " pdb=" O ASN C 624 " ideal model delta sigma weight residual 121.84 117.53 4.31 1.16e+00 7.43e-01 1.38e+01 ... (remaining 14679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 6222 21.92 - 43.84: 354 43.84 - 65.76: 56 65.76 - 87.67: 38 87.67 - 109.59: 50 Dihedral angle restraints: 6720 sinusoidal: 3004 harmonic: 3716 Sorted by residual: dihedral pdb=" CA ILE C 478 " pdb=" C ILE C 478 " pdb=" N CYS C 479 " pdb=" CA CYS C 479 " ideal model delta harmonic sigma weight residual -180.00 -158.63 -21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ILE A 478 " pdb=" C ILE A 478 " pdb=" N CYS A 479 " pdb=" CA CYS A 479 " ideal model delta harmonic sigma weight residual -180.00 -158.63 -21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CB CYS C 212 " pdb=" SG CYS C 212 " pdb=" SG CYS C 271 " pdb=" CB CYS C 271 " ideal model delta sinusoidal sigma weight residual 93.00 57.12 35.88 1 1.00e+01 1.00e-02 1.82e+01 ... (remaining 6717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1468 0.070 - 0.141: 238 0.141 - 0.211: 28 0.211 - 0.281: 2 0.281 - 0.352: 4 Chirality restraints: 1740 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 57 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 57 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 1737 not shown) Planarity restraints: 1780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 460 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C ILE C 460 " 0.054 2.00e-02 2.50e+03 pdb=" O ILE C 460 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN C 461 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 460 " 0.016 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C ILE A 460 " -0.054 2.00e-02 2.50e+03 pdb=" O ILE A 460 " 0.020 2.00e-02 2.50e+03 pdb=" N GLN A 461 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 457 " 0.045 5.00e-02 4.00e+02 6.69e-02 7.17e+00 pdb=" N PRO A 458 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 458 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 458 " 0.038 5.00e-02 4.00e+02 ... (remaining 1777 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 170 2.68 - 3.24: 9382 3.24 - 3.79: 15779 3.79 - 4.35: 22578 4.35 - 4.90: 36146 Nonbonded interactions: 84055 Sorted by model distance: nonbonded pdb=" OD1 ASP A 574 " pdb="ZN ZN A 901 " model vdw 2.126 2.230 nonbonded pdb=" OD1 ASP C 574 " pdb="ZN ZN C 901 " model vdw 2.126 2.230 nonbonded pdb=" O SER C 640 " pdb=" OG SER C 644 " model vdw 2.298 2.440 nonbonded pdb=" O SER A 640 " pdb=" OG SER A 644 " model vdw 2.298 2.440 nonbonded pdb=" OD1 ASN C 501 " pdb=" OG SER C 559 " model vdw 2.313 2.440 ... (remaining 84050 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 'C' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'O' selection = chain 'P' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 32.830 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.050 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:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 : 0.005 0.042 10770 Z= 0.296 Angle : 0.817 10.047 14684 Z= 0.452 Chirality : 0.055 0.352 1740 Planarity : 0.006 0.067 1772 Dihedral : 18.783 109.593 4296 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.18 % Allowed : 3.94 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -4.23 (0.19), residues: 1232 helix: -4.34 (0.09), residues: 552 sheet: 0.45 (0.29), residues: 280 loop : -2.56 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 754 HIS 0.004 0.001 HIS A 594 PHE 0.013 0.001 PHE C 193 TYR 0.015 0.002 TYR A 481 ARG 0.002 0.000 ARG C 289 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 294 time to evaluate : 1.131 Fit side-chains REVERT: A 517 ARG cc_start: 0.8020 (tmt170) cc_final: 0.7716 (ttp-170) REVERT: A 684 MET cc_start: 0.6582 (mmt) cc_final: 0.5214 (ttt) REVERT: A 695 TRP cc_start: 0.8404 (m-10) cc_final: 0.8056 (m-10) REVERT: A 708 ASP cc_start: 0.8277 (t0) cc_final: 0.7877 (t0) REVERT: C 101 LYS cc_start: 0.8960 (mttt) cc_final: 0.8686 (mmtt) REVERT: C 517 ARG cc_start: 0.8020 (tmt170) cc_final: 0.7716 (ttp-170) REVERT: C 684 MET cc_start: 0.6584 (mmt) cc_final: 0.5219 (ttt) REVERT: C 695 TRP cc_start: 0.8404 (m-10) cc_final: 0.8055 (m-10) REVERT: C 708 ASP cc_start: 0.8274 (t0) cc_final: 0.7877 (t0) outliers start: 2 outliers final: 2 residues processed: 296 average time/residue: 0.8570 time to fit residues: 279.4727 Evaluate side-chains 238 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 236 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain C residue 332 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 5.9990 chunk 93 optimal weight: 0.0980 chunk 52 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS A 447 ASN A 541 HIS A 763 GLN C 142 GLN C 229 HIS C 447 ASN C 541 HIS C 763 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10770 Z= 0.293 Angle : 0.696 8.103 14684 Z= 0.346 Chirality : 0.048 0.270 1740 Planarity : 0.005 0.042 1772 Dihedral : 14.602 84.962 2032 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.61 % Allowed : 15.50 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.77 (0.21), residues: 1232 helix: -1.69 (0.18), residues: 560 sheet: 1.10 (0.29), residues: 270 loop : -1.78 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 446 HIS 0.006 0.001 HIS C 594 PHE 0.016 0.002 PHE C 632 TYR 0.014 0.002 TYR A 81 ARG 0.002 0.000 ARG A 517 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 256 time to evaluate : 1.234 Fit side-chains REVERT: A 101 LYS cc_start: 0.9041 (mttt) cc_final: 0.8783 (mttm) REVERT: A 240 MET cc_start: 0.9558 (ttt) cc_final: 0.8977 (tmm) REVERT: A 320 PHE cc_start: 0.9096 (m-80) cc_final: 0.8868 (m-80) REVERT: A 517 ARG cc_start: 0.7776 (tmt170) cc_final: 0.7526 (ttp-170) REVERT: A 541 HIS cc_start: 0.8600 (m-70) cc_final: 0.8314 (m90) REVERT: A 720 ASN cc_start: 0.9137 (m-40) cc_final: 0.8774 (m110) REVERT: A 781 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8629 (mm-30) REVERT: C 101 LYS cc_start: 0.9043 (mttt) cc_final: 0.8784 (mttm) REVERT: C 142 GLN cc_start: 0.7914 (tp-100) cc_final: 0.7685 (tp40) REVERT: C 240 MET cc_start: 0.9557 (ttt) cc_final: 0.8977 (tmm) REVERT: C 320 PHE cc_start: 0.9095 (m-80) cc_final: 0.8867 (m-80) REVERT: C 517 ARG cc_start: 0.7774 (tmt170) cc_final: 0.7524 (ttp-170) REVERT: C 541 HIS cc_start: 0.8598 (m-70) cc_final: 0.8314 (m90) REVERT: C 720 ASN cc_start: 0.9139 (m-40) cc_final: 0.8775 (m110) REVERT: C 781 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8628 (mm-30) outliers start: 18 outliers final: 8 residues processed: 264 average time/residue: 0.9422 time to fit residues: 272.0965 Evaluate side-chains 232 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 224 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 750 THR Chi-restraints excluded: chain C residue 807 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 0.0020 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 112 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 594 HIS A 763 GLN C 594 HIS C 763 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10770 Z= 0.207 Angle : 0.611 8.194 14684 Z= 0.296 Chirality : 0.046 0.264 1740 Planarity : 0.004 0.038 1772 Dihedral : 10.918 64.181 2032 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.96 % Allowed : 16.49 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.41 (0.23), residues: 1232 helix: -0.03 (0.21), residues: 556 sheet: 1.35 (0.29), residues: 270 loop : -1.68 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 106 HIS 0.004 0.001 HIS A 594 PHE 0.019 0.001 PHE A 700 TYR 0.011 0.001 TYR C 81 ARG 0.005 0.000 ARG C 518 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 245 time to evaluate : 1.206 Fit side-chains REVERT: A 101 LYS cc_start: 0.9122 (mttt) cc_final: 0.8876 (mttm) REVERT: A 240 MET cc_start: 0.9600 (ttt) cc_final: 0.8948 (tmm) REVERT: A 524 ARG cc_start: 0.7559 (mtm-85) cc_final: 0.6742 (mmm160) REVERT: A 541 HIS cc_start: 0.8561 (m-70) cc_final: 0.8337 (m90) REVERT: A 548 MET cc_start: 0.8938 (mtm) cc_final: 0.8674 (mtp) REVERT: A 713 MET cc_start: 0.9302 (mmt) cc_final: 0.9017 (mmm) REVERT: A 720 ASN cc_start: 0.8980 (m-40) cc_final: 0.8610 (m110) REVERT: A 781 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8520 (mm-30) REVERT: C 101 LYS cc_start: 0.9123 (mttt) cc_final: 0.8876 (mttm) REVERT: C 142 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7720 (tp40) REVERT: C 240 MET cc_start: 0.9599 (ttt) cc_final: 0.8947 (tmm) REVERT: C 524 ARG cc_start: 0.7563 (mtm-85) cc_final: 0.6744 (mmm160) REVERT: C 541 HIS cc_start: 0.8562 (m-70) cc_final: 0.8337 (m90) REVERT: C 548 MET cc_start: 0.8938 (mtm) cc_final: 0.8672 (mtp) REVERT: C 713 MET cc_start: 0.9299 (mmt) cc_final: 0.9016 (mmm) REVERT: C 720 ASN cc_start: 0.8980 (m-40) cc_final: 0.8610 (m110) REVERT: C 781 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8516 (mm-30) outliers start: 33 outliers final: 12 residues processed: 260 average time/residue: 0.9738 time to fit residues: 276.5839 Evaluate side-chains 247 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 235 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 810 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 476 GLN A 763 GLN C 447 ASN C 476 GLN C 763 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 10770 Z= 0.358 Angle : 0.641 8.110 14684 Z= 0.318 Chirality : 0.047 0.276 1740 Planarity : 0.004 0.040 1772 Dihedral : 8.618 57.708 2032 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.23 % Allowed : 19.44 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.30 (0.23), residues: 1232 helix: 0.83 (0.22), residues: 558 sheet: 1.43 (0.28), residues: 268 loop : -1.56 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 106 HIS 0.004 0.001 HIS C 487 PHE 0.017 0.002 PHE C 632 TYR 0.016 0.002 TYR A 188 ARG 0.002 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 232 time to evaluate : 1.220 Fit side-chains REVERT: A 101 LYS cc_start: 0.9188 (mttt) cc_final: 0.8923 (mttm) REVERT: A 143 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8196 (mt0) REVERT: A 152 MET cc_start: 0.9380 (ttm) cc_final: 0.9149 (mtt) REVERT: A 195 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8279 (mtpm) REVERT: A 240 MET cc_start: 0.9612 (ttt) cc_final: 0.9090 (tmm) REVERT: A 524 ARG cc_start: 0.7509 (mtm-85) cc_final: 0.7232 (mmm-85) REVERT: A 555 GLU cc_start: 0.9030 (tp30) cc_final: 0.8601 (tp30) REVERT: A 577 PHE cc_start: 0.9315 (OUTLIER) cc_final: 0.8547 (m-80) REVERT: A 720 ASN cc_start: 0.8762 (m-40) cc_final: 0.8455 (m110) REVERT: A 781 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8541 (mm-30) REVERT: C 101 LYS cc_start: 0.9188 (mttt) cc_final: 0.8924 (mttm) REVERT: C 152 MET cc_start: 0.9380 (ttm) cc_final: 0.9150 (mtt) REVERT: C 195 LYS cc_start: 0.8567 (mtpp) cc_final: 0.8281 (mtpm) REVERT: C 240 MET cc_start: 0.9612 (ttt) cc_final: 0.9087 (tmm) REVERT: C 524 ARG cc_start: 0.7514 (mtm-85) cc_final: 0.7236 (mmm-85) REVERT: C 555 GLU cc_start: 0.9030 (tp30) cc_final: 0.8603 (tp30) REVERT: C 577 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.8546 (m-80) REVERT: C 720 ASN cc_start: 0.8762 (m-40) cc_final: 0.8455 (m110) REVERT: C 781 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8541 (mm-30) outliers start: 36 outliers final: 20 residues processed: 246 average time/residue: 1.0428 time to fit residues: 279.7218 Evaluate side-chains 248 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 225 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 810 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 107 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 541 HIS A 763 GLN C 447 ASN C 541 HIS C 763 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10770 Z= 0.205 Angle : 0.567 7.347 14684 Z= 0.278 Chirality : 0.044 0.273 1740 Planarity : 0.003 0.037 1772 Dihedral : 7.660 57.697 2032 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.05 % Allowed : 19.80 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.74 (0.24), residues: 1232 helix: 1.34 (0.23), residues: 556 sheet: 1.55 (0.28), residues: 270 loop : -1.49 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 106 HIS 0.003 0.001 HIS C 487 PHE 0.019 0.001 PHE A 700 TYR 0.011 0.001 TYR C 188 ARG 0.002 0.000 ARG C 518 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 236 time to evaluate : 1.168 Fit side-chains REVERT: A 101 LYS cc_start: 0.9180 (mttt) cc_final: 0.8911 (mttm) REVERT: A 143 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8098 (mt0) REVERT: A 152 MET cc_start: 0.9342 (ttm) cc_final: 0.9139 (mtt) REVERT: A 240 MET cc_start: 0.9601 (ttt) cc_final: 0.8984 (tmm) REVERT: A 524 ARG cc_start: 0.7608 (mtm-85) cc_final: 0.7361 (mmm-85) REVERT: A 555 GLU cc_start: 0.9006 (tp30) cc_final: 0.8542 (tp30) REVERT: A 588 LYS cc_start: 0.8889 (tptp) cc_final: 0.8659 (mmmt) REVERT: A 720 ASN cc_start: 0.8722 (m-40) cc_final: 0.8394 (m110) REVERT: C 101 LYS cc_start: 0.9178 (mttt) cc_final: 0.8910 (mttm) REVERT: C 143 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8102 (mt0) REVERT: C 152 MET cc_start: 0.9341 (ttm) cc_final: 0.9138 (mtt) REVERT: C 240 MET cc_start: 0.9600 (ttt) cc_final: 0.8983 (tmm) REVERT: C 524 ARG cc_start: 0.7610 (mtm-85) cc_final: 0.7363 (mmm-85) REVERT: C 555 GLU cc_start: 0.9006 (tp30) cc_final: 0.8539 (tp30) REVERT: C 588 LYS cc_start: 0.8892 (tptp) cc_final: 0.8664 (mmmt) REVERT: C 720 ASN cc_start: 0.8720 (m-40) cc_final: 0.8393 (m110) outliers start: 34 outliers final: 14 residues processed: 246 average time/residue: 0.9831 time to fit residues: 264.1012 Evaluate side-chains 238 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 222 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 810 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 23 optimal weight: 0.0970 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 0.0030 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 447 ASN A 461 GLN A 541 HIS C 121 ASN C 447 ASN C 461 GLN C 541 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10770 Z= 0.141 Angle : 0.542 7.294 14684 Z= 0.266 Chirality : 0.043 0.270 1740 Planarity : 0.003 0.033 1772 Dihedral : 6.792 56.485 2032 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.79 % Allowed : 21.59 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.24), residues: 1232 helix: 1.80 (0.23), residues: 552 sheet: 1.61 (0.28), residues: 270 loop : -1.35 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 768 HIS 0.002 0.000 HIS A 791 PHE 0.017 0.001 PHE C 632 TYR 0.013 0.001 TYR C 81 ARG 0.002 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 247 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LYS cc_start: 0.9136 (mttt) cc_final: 0.8888 (mttm) REVERT: A 113 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8470 (tp-100) REVERT: A 152 MET cc_start: 0.9327 (ttm) cc_final: 0.9125 (mtt) REVERT: A 219 ASN cc_start: 0.8619 (m-40) cc_final: 0.8417 (p0) REVERT: A 240 MET cc_start: 0.9595 (ttt) cc_final: 0.8951 (tmm) REVERT: A 524 ARG cc_start: 0.7581 (mtm-85) cc_final: 0.7334 (mtm-85) REVERT: A 555 GLU cc_start: 0.9008 (tp30) cc_final: 0.8453 (tp30) REVERT: A 720 ASN cc_start: 0.8911 (m-40) cc_final: 0.8492 (m110) REVERT: A 769 GLU cc_start: 0.8687 (mp0) cc_final: 0.8380 (mp0) REVERT: A 781 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8441 (mm-30) REVERT: C 101 LYS cc_start: 0.9151 (mttt) cc_final: 0.8907 (mttm) REVERT: C 142 GLN cc_start: 0.8073 (tp-100) cc_final: 0.7780 (tp40) REVERT: C 152 MET cc_start: 0.9327 (ttm) cc_final: 0.9125 (mtt) REVERT: C 219 ASN cc_start: 0.8620 (m-40) cc_final: 0.8420 (p0) REVERT: C 240 MET cc_start: 0.9595 (ttt) cc_final: 0.8952 (tmm) REVERT: C 524 ARG cc_start: 0.7584 (mtm-85) cc_final: 0.7338 (mtm-85) REVERT: C 555 GLU cc_start: 0.9005 (tp30) cc_final: 0.8449 (tp30) REVERT: C 720 ASN cc_start: 0.8909 (m-40) cc_final: 0.8489 (m110) REVERT: C 769 GLU cc_start: 0.8677 (mp0) cc_final: 0.8378 (mp0) REVERT: C 781 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8441 (mm-30) outliers start: 20 outliers final: 8 residues processed: 253 average time/residue: 0.9549 time to fit residues: 264.1527 Evaluate side-chains 232 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 224 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 807 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 143 GLN A 447 ASN A 461 GLN A 467 GLN A 497 ASN A 541 HIS A 636 HIS C 113 GLN C 121 ASN C 143 GLN C 447 ASN C 461 GLN C 467 GLN C 541 HIS C 636 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10770 Z= 0.210 Angle : 0.556 7.199 14684 Z= 0.273 Chirality : 0.044 0.267 1740 Planarity : 0.003 0.033 1772 Dihedral : 6.771 56.265 2032 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.97 % Allowed : 23.39 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.21 (0.24), residues: 1232 helix: 1.84 (0.23), residues: 552 sheet: 1.66 (0.29), residues: 270 loop : -1.33 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 768 HIS 0.004 0.001 HIS A 487 PHE 0.020 0.001 PHE C 632 TYR 0.015 0.001 TYR A 590 ARG 0.002 0.000 ARG C 518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 228 time to evaluate : 1.204 Fit side-chains REVERT: A 101 LYS cc_start: 0.9169 (mttt) cc_final: 0.8882 (mttm) REVERT: A 121 ASN cc_start: 0.8680 (m-40) cc_final: 0.8437 (m110) REVERT: A 143 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8138 (mt0) REVERT: A 152 MET cc_start: 0.9320 (ttm) cc_final: 0.9116 (mtt) REVERT: A 219 ASN cc_start: 0.8628 (m-40) cc_final: 0.8408 (p0) REVERT: A 240 MET cc_start: 0.9566 (ttt) cc_final: 0.8958 (tmm) REVERT: A 524 ARG cc_start: 0.7588 (mtm-85) cc_final: 0.7307 (mtm-85) REVERT: A 555 GLU cc_start: 0.9010 (tp30) cc_final: 0.8439 (tp30) REVERT: A 613 MET cc_start: 0.7990 (mtt) cc_final: 0.7640 (mpt) REVERT: A 720 ASN cc_start: 0.8901 (m-40) cc_final: 0.8584 (m110) REVERT: A 781 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8446 (mm-30) REVERT: C 101 LYS cc_start: 0.9169 (mttt) cc_final: 0.8881 (mttm) REVERT: C 121 ASN cc_start: 0.8680 (m-40) cc_final: 0.8436 (m110) REVERT: C 142 GLN cc_start: 0.8096 (tp-100) cc_final: 0.7811 (tp40) REVERT: C 143 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8131 (mt0) REVERT: C 152 MET cc_start: 0.9321 (ttm) cc_final: 0.9117 (mtt) REVERT: C 219 ASN cc_start: 0.8626 (m-40) cc_final: 0.8410 (p0) REVERT: C 240 MET cc_start: 0.9566 (ttt) cc_final: 0.8958 (tmm) REVERT: C 524 ARG cc_start: 0.7589 (mtm-85) cc_final: 0.7308 (mtm-85) REVERT: C 555 GLU cc_start: 0.9010 (tp30) cc_final: 0.8437 (tp30) REVERT: C 613 MET cc_start: 0.7990 (mtt) cc_final: 0.7638 (mpt) REVERT: C 720 ASN cc_start: 0.8899 (m-40) cc_final: 0.8584 (m110) REVERT: C 769 GLU cc_start: 0.8742 (mp0) cc_final: 0.8526 (mp0) REVERT: C 781 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8447 (mm-30) outliers start: 22 outliers final: 14 residues processed: 238 average time/residue: 0.9760 time to fit residues: 253.9063 Evaluate side-chains 233 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 217 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 810 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 36 optimal weight: 0.0570 chunk 23 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 447 ASN A 461 GLN A 763 GLN C 143 GLN C 447 ASN C 461 GLN C 763 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10770 Z= 0.320 Angle : 0.591 6.682 14684 Z= 0.294 Chirality : 0.045 0.269 1740 Planarity : 0.003 0.036 1772 Dihedral : 6.813 56.184 2032 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.51 % Allowed : 22.76 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.23 (0.24), residues: 1232 helix: 1.88 (0.23), residues: 552 sheet: 1.66 (0.29), residues: 270 loop : -1.34 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 768 HIS 0.004 0.001 HIS A 487 PHE 0.022 0.001 PHE A 632 TYR 0.019 0.002 TYR A 590 ARG 0.002 0.000 ARG C 776 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 213 time to evaluate : 1.104 Fit side-chains REVERT: A 101 LYS cc_start: 0.9179 (mttt) cc_final: 0.8881 (mttm) REVERT: A 152 MET cc_start: 0.9332 (ttm) cc_final: 0.9122 (mtt) REVERT: A 219 ASN cc_start: 0.8676 (m-40) cc_final: 0.8371 (p0) REVERT: A 240 MET cc_start: 0.9606 (ttt) cc_final: 0.8966 (tmm) REVERT: A 524 ARG cc_start: 0.7644 (mtm-85) cc_final: 0.7340 (mtm-85) REVERT: A 555 GLU cc_start: 0.9015 (tp30) cc_final: 0.8428 (tp30) REVERT: A 781 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8484 (mm-30) REVERT: C 101 LYS cc_start: 0.9178 (mttt) cc_final: 0.8888 (mttm) REVERT: C 142 GLN cc_start: 0.8065 (tp-100) cc_final: 0.7755 (tp40) REVERT: C 152 MET cc_start: 0.9332 (ttm) cc_final: 0.9122 (mtt) REVERT: C 219 ASN cc_start: 0.8673 (m-40) cc_final: 0.8373 (p0) REVERT: C 240 MET cc_start: 0.9607 (ttt) cc_final: 0.8967 (tmm) REVERT: C 524 ARG cc_start: 0.7646 (mtm-85) cc_final: 0.7341 (mtm-85) REVERT: C 555 GLU cc_start: 0.9016 (tp30) cc_final: 0.8427 (tp30) REVERT: C 781 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8483 (mm-30) outliers start: 28 outliers final: 18 residues processed: 229 average time/residue: 0.9892 time to fit residues: 249.5222 Evaluate side-chains 228 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 210 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 810 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 461 GLN A 497 ASN A 763 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 ASN C 461 GLN C 763 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10770 Z= 0.300 Angle : 0.591 6.687 14684 Z= 0.296 Chirality : 0.045 0.265 1740 Planarity : 0.003 0.037 1772 Dihedral : 6.808 56.278 2032 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.51 % Allowed : 23.57 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.28 (0.24), residues: 1232 helix: 1.92 (0.23), residues: 554 sheet: 1.65 (0.29), residues: 270 loop : -1.31 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 768 HIS 0.004 0.001 HIS C 487 PHE 0.023 0.001 PHE C 632 TYR 0.020 0.001 TYR A 590 ARG 0.001 0.000 ARG C 776 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 218 time to evaluate : 1.122 Fit side-chains REVERT: A 101 LYS cc_start: 0.9173 (mttt) cc_final: 0.8881 (mttm) REVERT: A 152 MET cc_start: 0.9328 (ttm) cc_final: 0.9122 (mtt) REVERT: A 240 MET cc_start: 0.9608 (ttt) cc_final: 0.8980 (tmm) REVERT: A 524 ARG cc_start: 0.7545 (mtm-85) cc_final: 0.7238 (mtm-85) REVERT: A 555 GLU cc_start: 0.9011 (tp30) cc_final: 0.8412 (tp30) REVERT: A 781 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8473 (mm-30) REVERT: C 101 LYS cc_start: 0.9188 (mttt) cc_final: 0.8900 (mttm) REVERT: C 142 GLN cc_start: 0.8101 (tp-100) cc_final: 0.7797 (tp40) REVERT: C 152 MET cc_start: 0.9328 (ttm) cc_final: 0.9121 (mtt) REVERT: C 219 ASN cc_start: 0.8672 (m-40) cc_final: 0.8363 (p0) REVERT: C 240 MET cc_start: 0.9607 (ttt) cc_final: 0.8981 (tmm) REVERT: C 524 ARG cc_start: 0.7545 (mtm-85) cc_final: 0.7240 (mtm-85) REVERT: C 555 GLU cc_start: 0.9011 (tp30) cc_final: 0.8412 (tp30) REVERT: C 781 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8470 (mm-30) outliers start: 28 outliers final: 20 residues processed: 236 average time/residue: 0.9390 time to fit residues: 242.7387 Evaluate side-chains 230 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 210 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 721 LEU Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 807 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 461 GLN A 763 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 ASN C 461 GLN C 763 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10770 Z= 0.218 Angle : 0.574 6.916 14684 Z= 0.286 Chirality : 0.044 0.258 1740 Planarity : 0.003 0.035 1772 Dihedral : 6.689 56.419 2032 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.97 % Allowed : 24.55 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.30 (0.24), residues: 1232 helix: 1.96 (0.23), residues: 552 sheet: 1.64 (0.29), residues: 270 loop : -1.30 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 768 HIS 0.003 0.001 HIS A 487 PHE 0.024 0.001 PHE C 632 TYR 0.016 0.001 TYR A 590 ARG 0.004 0.000 ARG C 734 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 210 time to evaluate : 1.083 Fit side-chains REVERT: A 101 LYS cc_start: 0.9165 (mttt) cc_final: 0.8870 (mttm) REVERT: A 152 MET cc_start: 0.9314 (ttm) cc_final: 0.9106 (mtt) REVERT: A 219 ASN cc_start: 0.8652 (m-40) cc_final: 0.8366 (p0) REVERT: A 240 MET cc_start: 0.9600 (ttt) cc_final: 0.8916 (tmm) REVERT: A 524 ARG cc_start: 0.7539 (mtm-85) cc_final: 0.7224 (mtm-85) REVERT: A 555 GLU cc_start: 0.9003 (tp30) cc_final: 0.8404 (tp30) REVERT: A 586 MET cc_start: 0.8639 (mmm) cc_final: 0.8270 (mpp) REVERT: A 781 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8461 (mm-30) REVERT: C 101 LYS cc_start: 0.9162 (mttt) cc_final: 0.8868 (mttm) REVERT: C 142 GLN cc_start: 0.8100 (tp-100) cc_final: 0.7798 (tp40) REVERT: C 152 MET cc_start: 0.9314 (ttm) cc_final: 0.9107 (mtt) REVERT: C 219 ASN cc_start: 0.8647 (m-40) cc_final: 0.8371 (p0) REVERT: C 240 MET cc_start: 0.9600 (ttt) cc_final: 0.8914 (tmm) REVERT: C 524 ARG cc_start: 0.7541 (mtm-85) cc_final: 0.7227 (mtm-85) REVERT: C 555 GLU cc_start: 0.9004 (tp30) cc_final: 0.8405 (tp30) REVERT: C 586 MET cc_start: 0.8640 (mmm) cc_final: 0.8272 (mpp) REVERT: C 781 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8460 (mm-30) outliers start: 22 outliers final: 20 residues processed: 222 average time/residue: 0.9057 time to fit residues: 220.6645 Evaluate side-chains 230 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 210 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 332 TYR Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 721 LEU Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 807 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 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 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 461 GLN A 763 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 ASN C 461 GLN C 763 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.132264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.089188 restraints weight = 13452.287| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.63 r_work: 0.2771 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10770 Z= 0.295 Angle : 0.593 6.723 14684 Z= 0.297 Chirality : 0.045 0.261 1740 Planarity : 0.003 0.037 1772 Dihedral : 6.706 56.445 2032 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.42 % Allowed : 24.01 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.28 (0.24), residues: 1232 helix: 1.93 (0.23), residues: 554 sheet: 1.64 (0.29), residues: 270 loop : -1.30 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 768 HIS 0.004 0.001 HIS C 487 PHE 0.025 0.002 PHE C 632 TYR 0.015 0.002 TYR A 590 ARG 0.004 0.000 ARG C 734 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4446.16 seconds wall clock time: 78 minutes 16.85 seconds (4696.85 seconds total)