Starting phenix.real_space_refine on Sun Dec 10 06:41:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irx_8117/12_2023/5irx_8117_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irx_8117/12_2023/5irx_8117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irx_8117/12_2023/5irx_8117.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irx_8117/12_2023/5irx_8117.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irx_8117/12_2023/5irx_8117_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irx_8117/12_2023/5irx_8117_trim_updated.pdb" } resolution = 2.95 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= 1.000 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 P 16 5.49 5 S 90 5.16 5 C 8710 2.51 5 N 2098 2.21 5 O 2248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 428": "NH1" <-> "NH2" Residue "A TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 491": "NH1" <-> "NH2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A ARG 743": "NH1" <-> "NH2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B ARG 579": "NH1" <-> "NH2" Residue "B ARG 743": "NH1" <-> "NH2" Residue "C ARG 428": "NH1" <-> "NH2" Residue "C TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 491": "NH1" <-> "NH2" Residue "C ARG 579": "NH1" <-> "NH2" Residue "C ARG 743": "NH1" <-> "NH2" Residue "D ARG 428": "NH1" <-> "NH2" Residue "D TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D ARG 579": "NH1" <-> "NH2" Residue "D ARG 743": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13162 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2893 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 108} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 466 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 195 Chain: "B" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2893 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 108} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 466 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 195 Chain: "C" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2893 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 108} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 466 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 195 Chain: "D" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2893 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 108} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 466 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 195 Chain: "E" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 493 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 68} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "F" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 493 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 68} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'6EU': 1, '6O8': 1, '6OE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 102 Unusual residues: {'6EU': 1, '6O8': 1, '6OE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 102 Unusual residues: {'6EU': 1, '6O8': 1, '6OE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Unusual residues: {'6EU': 1, '6O8': 1, '6O9': 1, '6OE': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'6O9': 1, '6OE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {'6O9': 2, '6OE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.61, per 1000 atoms: 0.58 Number of scatterers: 13162 At special positions: 0 Unit cell: (120.344, 120.344, 110.62, 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) S 90 16.00 P 16 15.00 O 2248 8.00 N 2098 7.00 C 8710 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 16 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 23 " distance=2.04 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 31 " distance=2.03 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 51 " - pdb=" SG CYS E 63 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 71 " distance=2.03 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 16 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 23 " distance=2.04 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 31 " distance=2.03 Simple disulfide: pdb=" SG CYS F 44 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 51 " - pdb=" SG CYS F 63 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 71 " 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.34 Conformation dependent library (CDL) restraints added in 2.4 seconds 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3228 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 4 sheets defined 54.2% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 336 through 343 removed outlier: 3.591A pdb=" N SER A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 412 through 415 No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.769A pdb=" N GLN A 423 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 453 Processing helix chain 'A' and resid 469 through 498 removed outlier: 3.559A pdb=" N PHE A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 531 removed outlier: 3.514A pdb=" N LEU A 515 " --> pdb=" O TYR A 511 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE A 516 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 554 removed outlier: 3.730A pdb=" N VAL A 538 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 539 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 543 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET A 547 " --> pdb=" O SER A 544 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP A 549 " --> pdb=" O ALA A 546 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A 551 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 553 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 574 removed outlier: 3.565A pdb=" N VAL A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 598 removed outlier: 4.288A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 585 " --> pdb=" O MET A 581 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE A 587 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 removed outlier: 3.530A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 removed outlier: 4.080A pdb=" N LEU A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 691 removed outlier: 3.581A pdb=" N ILE A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 696 No H-bonds generated for 'chain 'A' and resid 693 through 696' Processing helix chain 'A' and resid 698 through 712 removed outlier: 3.900A pdb=" N PHE A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 719 No H-bonds generated for 'chain 'A' and resid 716 through 719' Processing helix chain 'B' and resid 336 through 343 removed outlier: 3.592A pdb=" N SER B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 412 through 415 No H-bonds generated for 'chain 'B' and resid 412 through 415' Processing helix chain 'B' and resid 419 through 428 removed outlier: 3.768A pdb=" N GLN B 423 " --> pdb=" O ASN B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 469 through 498 removed outlier: 3.560A pdb=" N PHE B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 475 " --> pdb=" O ASP B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 531 removed outlier: 3.514A pdb=" N LEU B 515 " --> pdb=" O TYR B 511 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 516 " --> pdb=" O SER B 512 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 554 removed outlier: 3.730A pdb=" N VAL B 538 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 539 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 543 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET B 547 " --> pdb=" O SER B 544 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP B 549 " --> pdb=" O ALA B 546 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B 551 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 553 " --> pdb=" O THR B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 574 removed outlier: 3.565A pdb=" N VAL B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 573 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 598 removed outlier: 4.289A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 585 " --> pdb=" O MET B 581 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 removed outlier: 3.530A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 removed outlier: 4.080A pdb=" N LEU B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 691 removed outlier: 3.580A pdb=" N ILE B 689 " --> pdb=" O THR B 685 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 696 No H-bonds generated for 'chain 'B' and resid 693 through 696' Processing helix chain 'B' and resid 698 through 712 removed outlier: 3.898A pdb=" N PHE B 712 " --> pdb=" O THR B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 719 No H-bonds generated for 'chain 'B' and resid 716 through 719' Processing helix chain 'C' and resid 336 through 343 removed outlier: 3.593A pdb=" N SER C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 412 through 415 No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 428 removed outlier: 3.768A pdb=" N GLN C 423 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 469 through 498 removed outlier: 3.560A pdb=" N PHE C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 475 " --> pdb=" O ASP C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 531 removed outlier: 3.514A pdb=" N LEU C 515 " --> pdb=" O TYR C 511 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE C 516 " --> pdb=" O SER C 512 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE C 531 " --> pdb=" O VAL C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 554 removed outlier: 3.730A pdb=" N VAL C 538 " --> pdb=" O LYS C 535 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 539 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE C 543 " --> pdb=" O SER C 540 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA C 546 " --> pdb=" O PHE C 543 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET C 547 " --> pdb=" O SER C 544 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP C 549 " --> pdb=" O ALA C 546 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN C 551 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 553 " --> pdb=" O THR C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 574 removed outlier: 3.565A pdb=" N VAL C 567 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU C 570 " --> pdb=" O ALA C 566 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 573 " --> pdb=" O ILE C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 598 removed outlier: 4.288A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 585 " --> pdb=" O MET C 581 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 586 " --> pdb=" O PHE C 582 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE C 587 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C 597 " --> pdb=" O THR C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 3.529A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 removed outlier: 4.080A pdb=" N LEU C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 691 removed outlier: 3.581A pdb=" N ILE C 689 " --> pdb=" O THR C 685 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 696 No H-bonds generated for 'chain 'C' and resid 693 through 696' Processing helix chain 'C' and resid 698 through 712 removed outlier: 3.899A pdb=" N PHE C 712 " --> pdb=" O THR C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 719 No H-bonds generated for 'chain 'C' and resid 716 through 719' Processing helix chain 'D' and resid 336 through 343 removed outlier: 3.592A pdb=" N SER D 343 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 412 through 415 No H-bonds generated for 'chain 'D' and resid 412 through 415' Processing helix chain 'D' and resid 419 through 428 removed outlier: 3.769A pdb=" N GLN D 423 " --> pdb=" O ASN D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 453 Processing helix chain 'D' and resid 469 through 498 removed outlier: 3.560A pdb=" N PHE D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 475 " --> pdb=" O ASP D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 531 removed outlier: 3.514A pdb=" N LEU D 515 " --> pdb=" O TYR D 511 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 516 " --> pdb=" O SER D 512 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE D 531 " --> pdb=" O VAL D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 554 removed outlier: 3.730A pdb=" N VAL D 538 " --> pdb=" O LYS D 535 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 539 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE D 543 " --> pdb=" O SER D 540 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA D 546 " --> pdb=" O PHE D 543 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET D 547 " --> pdb=" O SER D 544 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP D 549 " --> pdb=" O ALA D 546 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN D 551 " --> pdb=" O GLY D 548 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 553 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 574 removed outlier: 3.565A pdb=" N VAL D 567 " --> pdb=" O GLY D 563 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU D 570 " --> pdb=" O ALA D 566 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 573 " --> pdb=" O ILE D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 598 removed outlier: 4.287A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 585 " --> pdb=" O MET D 581 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL D 586 " --> pdb=" O PHE D 582 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE D 587 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 removed outlier: 3.529A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 removed outlier: 4.080A pdb=" N LEU D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 691 removed outlier: 3.580A pdb=" N ILE D 689 " --> pdb=" O THR D 685 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 696 No H-bonds generated for 'chain 'D' and resid 693 through 696' Processing helix chain 'D' and resid 698 through 712 removed outlier: 3.900A pdb=" N PHE D 712 " --> pdb=" O THR D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 719 No H-bonds generated for 'chain 'D' and resid 716 through 719' Processing sheet with id= A, first strand: chain 'A' and resid 743 through 746 removed outlier: 6.099A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 743 through 746 removed outlier: 6.099A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 743 through 746 removed outlier: 6.099A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 743 through 746 removed outlier: 6.099A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1632 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: 3.28 Time building geometry restraints manager: 5.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1902 1.30 - 1.44: 4159 1.44 - 1.58: 7249 1.58 - 1.71: 32 1.71 - 1.85: 144 Bond restraints: 13486 Sorted by residual: bond pdb=" CAV 6EU D 805 " pdb=" CBB 6EU D 805 " ideal model delta sigma weight residual 1.330 1.524 -0.194 2.00e-02 2.50e+03 9.41e+01 bond pdb=" CAV 6EU C 803 " pdb=" CBB 6EU C 803 " ideal model delta sigma weight residual 1.330 1.524 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" CAV 6EU B 803 " pdb=" CBB 6EU B 803 " ideal model delta sigma weight residual 1.330 1.524 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" CAV 6EU A 804 " pdb=" CBB 6EU A 804 " ideal model delta sigma weight residual 1.330 1.524 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" CAR 6EU B 803 " pdb=" CAZ 6EU B 803 " ideal model delta sigma weight residual 1.538 1.373 0.165 2.00e-02 2.50e+03 6.83e+01 ... (remaining 13481 not shown) Histogram of bond angle deviations from ideal: 95.48 - 105.62: 226 105.62 - 115.77: 8067 115.77 - 125.91: 9842 125.91 - 136.05: 201 136.05 - 146.19: 4 Bond angle restraints: 18340 Sorted by residual: angle pdb=" C CYS F 23 " pdb=" N PRO F 24 " pdb=" CA PRO F 24 " ideal model delta sigma weight residual 127.00 146.19 -19.19 2.40e+00 1.74e-01 6.40e+01 angle pdb=" C CYS E 23 " pdb=" N PRO E 24 " pdb=" CA PRO E 24 " ideal model delta sigma weight residual 127.00 146.15 -19.15 2.40e+00 1.74e-01 6.37e+01 angle pdb=" C CYS F 23 " pdb=" N PRO F 24 " pdb=" CD PRO F 24 " ideal model delta sigma weight residual 120.60 105.11 15.49 2.20e+00 2.07e-01 4.96e+01 angle pdb=" C CYS E 23 " pdb=" N PRO E 24 " pdb=" CD PRO E 24 " ideal model delta sigma weight residual 120.60 105.15 15.45 2.20e+00 2.07e-01 4.93e+01 angle pdb=" O04 6O9 E 101 " pdb=" P05 6O9 E 101 " pdb=" O08 6O9 E 101 " ideal model delta sigma weight residual 93.00 108.99 -15.99 3.00e+00 1.11e-01 2.84e+01 ... (remaining 18335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 7865 34.85 - 69.70: 134 69.70 - 104.54: 37 104.54 - 139.39: 29 139.39 - 174.24: 23 Dihedral angle restraints: 8088 sinusoidal: 3036 harmonic: 5052 Sorted by residual: dihedral pdb=" CA GLU A 416 " pdb=" C GLU A 416 " pdb=" N PRO A 417 " pdb=" CA PRO A 417 " ideal model delta harmonic sigma weight residual 180.00 133.67 46.33 0 5.00e+00 4.00e-02 8.59e+01 dihedral pdb=" CA GLU C 416 " pdb=" C GLU C 416 " pdb=" N PRO C 417 " pdb=" CA PRO C 417 " ideal model delta harmonic sigma weight residual 180.00 133.70 46.30 0 5.00e+00 4.00e-02 8.58e+01 dihedral pdb=" CA GLU B 416 " pdb=" C GLU B 416 " pdb=" N PRO B 417 " pdb=" CA PRO B 417 " ideal model delta harmonic sigma weight residual 180.00 133.72 46.28 0 5.00e+00 4.00e-02 8.57e+01 ... (remaining 8085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1639 0.079 - 0.157: 343 0.157 - 0.236: 38 0.236 - 0.314: 10 0.314 - 0.393: 8 Chirality restraints: 2038 Sorted by residual: chirality pdb=" CAR 6EU A 804 " pdb=" CAO 6EU A 804 " pdb=" CAU 6EU A 804 " pdb=" CAZ 6EU A 804 " both_signs ideal model delta sigma weight residual False 2.83 2.44 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CAR 6EU C 803 " pdb=" CAO 6EU C 803 " pdb=" CAU 6EU C 803 " pdb=" CAZ 6EU C 803 " both_signs ideal model delta sigma weight residual False 2.83 2.44 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CAR 6EU D 805 " pdb=" CAO 6EU D 805 " pdb=" CAU 6EU D 805 " pdb=" CAZ 6EU D 805 " both_signs ideal model delta sigma weight residual False 2.83 2.44 0.39 2.00e-01 2.50e+01 3.84e+00 ... (remaining 2035 not shown) Planarity restraints: 2224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 455 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO B 456 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 456 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 456 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 455 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO D 456 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 456 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 456 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 455 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO C 456 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 456 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 456 " -0.035 5.00e-02 4.00e+02 ... (remaining 2221 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.38: 32 2.38 - 3.01: 6678 3.01 - 3.64: 19147 3.64 - 4.27: 29079 4.27 - 4.90: 47636 Nonbonded interactions: 102572 Sorted by model distance: nonbonded pdb=" O GLU F 26 " pdb=" O07 6OE F 103 " model vdw 1.744 3.040 nonbonded pdb=" O GLU E 26 " pdb=" O07 6OE E 102 " model vdw 1.819 3.040 nonbonded pdb=" OD1 ASN B 437 " pdb=" O06 6O8 B 801 " model vdw 2.134 3.040 nonbonded pdb=" OD1 ASN A 437 " pdb=" O06 6O8 A 801 " model vdw 2.161 3.040 nonbonded pdb=" OD1 ASN C 437 " pdb=" O06 6O8 C 801 " model vdw 2.162 3.040 ... (remaining 102567 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' and (resid 335 through 751 or resid 801)) selection = (chain 'B' and (resid 335 through 751 or resid 801)) selection = (chain 'C' and (resid 335 through 751 or resid 801)) selection = (chain 'D' and (resid 335 through 751 or resid 801)) } ncs_group { reference = (chain 'E' and (resid 1 through 75 or resid 101)) selection = (chain 'F' and (resid 1 through 75 or resid 101)) } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 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: 2.270 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 37.040 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.080 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:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 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 : 0.014 0.194 13486 Z= 0.942 Angle : 1.437 19.195 18340 Z= 0.660 Chirality : 0.067 0.393 2038 Planarity : 0.006 0.063 2224 Dihedral : 19.899 174.240 4824 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.68 % Favored : 89.21 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -6.45 (0.12), residues: 1714 helix: -4.13 (0.08), residues: 988 sheet: -4.38 (0.62), residues: 52 loop : -4.31 (0.17), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP E 53 HIS 0.004 0.001 HIS C 358 PHE 0.034 0.003 PHE D 448 TYR 0.022 0.003 TYR C 653 ARG 0.010 0.002 ARG D 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 1.3907 time to fit residues: 432.0403 Evaluate side-chains 189 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.524 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 40.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 628 ASN A 691 GLN B 628 ASN B 691 GLN C 628 ASN C 691 GLN D 437 ASN D 494 GLN D 628 ASN D 691 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13486 Z= 0.189 Angle : 0.605 8.075 18340 Z= 0.304 Chirality : 0.039 0.186 2038 Planarity : 0.005 0.062 2224 Dihedral : 19.270 174.569 2612 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.17 % Allowed : 14.40 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -4.07 (0.16), residues: 1714 helix: -1.81 (0.13), residues: 1008 sheet: -4.55 (0.50), residues: 64 loop : -3.91 (0.19), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 749 HIS 0.001 0.000 HIS B 410 PHE 0.013 0.001 PHE B 448 TYR 0.016 0.001 TYR E 22 ARG 0.003 0.001 ARG D 474 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 256 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 11 residues processed: 264 average time/residue: 0.9562 time to fit residues: 282.7629 Evaluate side-chains 219 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 208 time to evaluate : 1.556 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 3 residues processed: 8 average time/residue: 0.2530 time to fit residues: 4.7670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 154 optimal weight: 40.0000 chunk 167 optimal weight: 0.0470 chunk 137 optimal weight: 2.9990 chunk 153 optimal weight: 30.0000 chunk 52 optimal weight: 30.0000 chunk 124 optimal weight: 10.0000 overall best weight: 2.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 494 GLN A 687 ASN B 437 ASN B 494 GLN C 354 GLN C 437 ASN C 494 GLN D 494 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13486 Z= 0.317 Angle : 0.656 8.852 18340 Z= 0.322 Chirality : 0.042 0.177 2038 Planarity : 0.004 0.056 2224 Dihedral : 16.530 156.567 2612 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 4.32 % Allowed : 17.08 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -2.85 (0.18), residues: 1714 helix: -0.57 (0.16), residues: 1016 sheet: -3.80 (0.63), residues: 52 loop : -3.95 (0.18), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 740 HIS 0.002 0.001 HIS A 358 PHE 0.016 0.002 PHE A 448 TYR 0.015 0.002 TYR C 653 ARG 0.003 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 215 time to evaluate : 1.550 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 18 residues processed: 230 average time/residue: 1.1791 time to fit residues: 297.2429 Evaluate side-chains 220 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 202 time to evaluate : 1.769 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 8 residues processed: 11 average time/residue: 0.5404 time to fit residues: 9.1303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 155 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 147 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 494 GLN A 691 GLN B 354 GLN B 494 GLN B 691 GLN C 354 GLN C 494 GLN C 691 GLN D 354 GLN D 494 GLN D 691 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13486 Z= 0.375 Angle : 0.660 8.920 18340 Z= 0.324 Chirality : 0.043 0.171 2038 Planarity : 0.004 0.056 2224 Dihedral : 15.604 117.619 2612 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 5.18 % Allowed : 19.19 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -2.24 (0.19), residues: 1714 helix: -0.03 (0.16), residues: 1004 sheet: -3.65 (0.61), residues: 52 loop : -3.73 (0.19), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 740 HIS 0.004 0.001 HIS B 358 PHE 0.016 0.002 PHE B 448 TYR 0.015 0.002 TYR E 22 ARG 0.003 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 201 time to evaluate : 1.453 Fit side-chains outliers start: 54 outliers final: 15 residues processed: 225 average time/residue: 1.2067 time to fit residues: 297.0723 Evaluate side-chains 213 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 198 time to evaluate : 1.518 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 7 residues processed: 8 average time/residue: 0.4521 time to fit residues: 6.3600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 147 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 691 GLN B 354 GLN B 691 GLN C 354 GLN C 691 GLN D 354 GLN D 687 ASN D 691 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13486 Z= 0.248 Angle : 0.619 12.624 18340 Z= 0.305 Chirality : 0.041 0.236 2038 Planarity : 0.004 0.053 2224 Dihedral : 15.018 121.184 2612 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 4.61 % Allowed : 21.31 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.12 % 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: -1.76 (0.20), residues: 1714 helix: 0.47 (0.17), residues: 988 sheet: -3.91 (0.54), residues: 64 loop : -3.57 (0.20), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 749 HIS 0.002 0.001 HIS F 30 PHE 0.010 0.001 PHE C 448 TYR 0.021 0.001 TYR F 22 ARG 0.002 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 210 time to evaluate : 1.562 Fit side-chains outliers start: 48 outliers final: 22 residues processed: 231 average time/residue: 1.1335 time to fit residues: 288.4815 Evaluate side-chains 222 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 200 time to evaluate : 1.362 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 11 residues processed: 11 average time/residue: 0.4794 time to fit residues: 8.1922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 76 optimal weight: 40.0000 chunk 13 optimal weight: 20.0000 chunk 54 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN B 354 GLN B 691 GLN C 354 GLN C 691 GLN D 354 GLN D 687 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13486 Z= 0.212 Angle : 0.591 9.006 18340 Z= 0.291 Chirality : 0.040 0.226 2038 Planarity : 0.004 0.053 2224 Dihedral : 14.263 117.687 2612 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 4.03 % Allowed : 22.84 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -1.34 (0.21), residues: 1714 helix: 0.77 (0.17), residues: 984 sheet: -3.53 (0.51), residues: 84 loop : -3.27 (0.21), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 11 HIS 0.002 0.001 HIS C 358 PHE 0.009 0.001 PHE D 448 TYR 0.019 0.001 TYR E 22 ARG 0.001 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 212 time to evaluate : 1.491 Fit side-chains outliers start: 42 outliers final: 18 residues processed: 236 average time/residue: 1.0874 time to fit residues: 283.5362 Evaluate side-chains 222 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 204 time to evaluate : 1.350 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 6 average time/residue: 0.5210 time to fit residues: 5.6409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 0.4980 chunk 120 optimal weight: 0.5980 chunk 138 optimal weight: 0.8980 chunk 91 optimal weight: 20.0000 chunk 163 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 GLN B 687 ASN C 354 GLN D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 13486 Z= 0.159 Angle : 0.575 11.256 18340 Z= 0.283 Chirality : 0.039 0.214 2038 Planarity : 0.003 0.052 2224 Dihedral : 13.765 118.433 2612 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.78 % Allowed : 24.38 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.12 % 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 (0.21), residues: 1714 helix: 0.91 (0.17), residues: 1020 sheet: -3.53 (0.50), residues: 84 loop : -3.55 (0.21), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 11 HIS 0.002 0.000 HIS C 358 PHE 0.006 0.001 PHE A 489 TYR 0.017 0.001 TYR F 22 ARG 0.001 0.000 ARG D 420 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 237 time to evaluate : 1.631 Fit side-chains outliers start: 29 outliers final: 12 residues processed: 249 average time/residue: 1.0548 time to fit residues: 291.0564 Evaluate side-chains 237 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 225 time to evaluate : 1.339 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.4869 time to fit residues: 3.5214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 0.0570 chunk 81 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 GLN D 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 13486 Z= 0.153 Angle : 0.562 9.329 18340 Z= 0.279 Chirality : 0.039 0.187 2038 Planarity : 0.003 0.053 2224 Dihedral : 13.353 117.080 2612 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.78 % Allowed : 25.91 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.98 (0.21), residues: 1714 helix: 1.13 (0.16), residues: 1020 sheet: -3.53 (0.49), residues: 84 loop : -3.48 (0.22), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 549 HIS 0.003 0.000 HIS E 30 PHE 0.006 0.001 PHE D 429 TYR 0.019 0.001 TYR E 22 ARG 0.001 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 233 time to evaluate : 1.543 Fit side-chains outliers start: 29 outliers final: 8 residues processed: 247 average time/residue: 1.1061 time to fit residues: 302.8534 Evaluate side-chains 233 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 225 time to evaluate : 1.459 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.2177 time to fit residues: 2.3426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 46 optimal weight: 0.0060 chunk 137 optimal weight: 0.5980 chunk 144 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 161 optimal weight: 0.0060 overall best weight: 0.5214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 GLN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 13486 Z= 0.148 Angle : 0.558 8.922 18340 Z= 0.277 Chirality : 0.039 0.185 2038 Planarity : 0.003 0.049 2224 Dihedral : 12.964 117.876 2612 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 1.82 % Allowed : 27.83 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.21), residues: 1714 helix: 1.37 (0.16), residues: 1020 sheet: -3.47 (0.49), residues: 84 loop : -3.42 (0.22), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 11 HIS 0.002 0.000 HIS E 30 PHE 0.014 0.001 PHE D 582 TYR 0.013 0.001 TYR F 34 ARG 0.001 0.000 ARG B 534 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 242 time to evaluate : 1.552 Fit side-chains outliers start: 19 outliers final: 7 residues processed: 252 average time/residue: 1.0198 time to fit residues: 285.7554 Evaluate side-chains 236 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 229 time to evaluate : 1.415 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.8850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 5.9990 chunk 76 optimal weight: 50.0000 chunk 112 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 155 optimal weight: 0.0870 chunk 134 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN B 354 GLN C 691 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13486 Z= 0.209 Angle : 0.606 10.592 18340 Z= 0.298 Chirality : 0.040 0.187 2038 Planarity : 0.003 0.047 2224 Dihedral : 12.868 116.646 2612 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 1.44 % Allowed : 30.33 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.64 (0.21), residues: 1714 helix: 1.43 (0.16), residues: 1004 sheet: -3.44 (0.49), residues: 84 loop : -3.27 (0.22), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 11 HIS 0.002 0.001 HIS E 30 PHE 0.010 0.001 PHE C 582 TYR 0.011 0.001 TYR A 653 ARG 0.003 0.000 ARG C 534 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 214 time to evaluate : 1.446 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 223 average time/residue: 1.1397 time to fit residues: 279.8848 Evaluate side-chains 220 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 211 time to evaluate : 1.457 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.6344 time to fit residues: 3.4099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.0070 chunk 135 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 118 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 GLN D 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.136391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.101520 restraints weight = 21264.282| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.57 r_work: 0.3149 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 13486 Z= 0.147 Angle : 0.568 9.215 18340 Z= 0.280 Chirality : 0.039 0.185 2038 Planarity : 0.003 0.051 2224 Dihedral : 12.303 119.970 2612 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 1.25 % Allowed : 30.71 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.43 (0.21), residues: 1714 helix: 1.62 (0.16), residues: 1004 sheet: -3.38 (0.50), residues: 84 loop : -3.22 (0.22), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 11 HIS 0.002 0.000 HIS B 358 PHE 0.011 0.001 PHE C 582 TYR 0.012 0.001 TYR A 631 ARG 0.002 0.000 ARG D 534 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4912.60 seconds wall clock time: 87 minutes 25.88 seconds (5245.88 seconds total)