Starting phenix.real_space_refine on Mon Mar 18 20:34:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7om0_12982/03_2024/7om0_12982_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7om0_12982/03_2024/7om0_12982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7om0_12982/03_2024/7om0_12982.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7om0_12982/03_2024/7om0_12982.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7om0_12982/03_2024/7om0_12982_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7om0_12982/03_2024/7om0_12982_updated.pdb" } resolution = 3.1 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= 0.001 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 18 5.49 5 S 66 5.16 5 C 14072 2.51 5 N 3676 2.21 5 O 4210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 333": "OE1" <-> "OE2" Residue "F PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 564": "OD1" <-> "OD2" Residue "F ASP 572": "OD1" <-> "OD2" Residue "F PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 572": "OD1" <-> "OD2" Residue "D PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 572": "OD1" <-> "OD2" Residue "E PHE 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22042 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3644 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3644 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3644 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3636 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 426} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3644 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3644 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.62, per 1000 atoms: 0.53 Number of scatterers: 22042 At special positions: 0 Unit cell: (132.02, 118.9, 130.38, 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 66 16.00 P 18 15.00 O 4210 8.00 N 3676 7.00 C 14072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 8.34 Conformation dependent library (CDL) restraints added in 3.7 seconds 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5050 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 103 helices and 24 sheets defined 39.3% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.44 Creating SS restraints... Processing helix chain 'A' and resid 317 through 338 Processing helix chain 'A' and resid 350 through 360 Processing helix chain 'A' and resid 388 through 398 removed outlier: 3.607A pdb=" N LEU A 398 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'A' and resid 487 through 501 Processing helix chain 'A' and resid 521 through 531 Processing helix chain 'A' and resid 542 through 544 No H-bonds generated for 'chain 'A' and resid 542 through 544' Processing helix chain 'A' and resid 551 through 554 Processing helix chain 'A' and resid 575 through 582 Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.523A pdb=" N ARG A 624 " --> pdb=" O GLY A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 651 through 663 Processing helix chain 'A' and resid 674 through 686 WARNING: missing atoms! Processing helix chain 'A' and resid 688 through 694 Processing helix chain 'A' and resid 707 through 719 removed outlier: 6.101A pdb=" N PHE A 713 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N TYR A 714 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS A 715 " --> pdb=" O TYR A 711 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU A 716 " --> pdb=" O ALA A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'B' and resid 317 through 338 Processing helix chain 'B' and resid 350 through 360 Processing helix chain 'B' and resid 388 through 398 Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 475 through 482 Processing helix chain 'B' and resid 487 through 501 Processing helix chain 'B' and resid 521 through 531 Processing helix chain 'B' and resid 551 through 556 removed outlier: 3.784A pdb=" N GLY B 556 " --> pdb=" O VAL B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 582 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 641 through 645 Processing helix chain 'B' and resid 647 through 649 No H-bonds generated for 'chain 'B' and resid 647 through 649' Processing helix chain 'B' and resid 651 through 663 Processing helix chain 'B' and resid 674 through 686 WARNING: missing atoms! Processing helix chain 'B' and resid 688 through 694 Processing helix chain 'B' and resid 707 through 719 removed outlier: 6.261A pdb=" N PHE B 713 " --> pdb=" O ILE B 709 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N TYR B 714 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS B 715 " --> pdb=" O TYR B 711 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP B 719 " --> pdb=" O LYS B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 736 Processing helix chain 'F' and resid 317 through 338 Processing helix chain 'F' and resid 350 through 360 Processing helix chain 'F' and resid 388 through 398 Processing helix chain 'F' and resid 404 through 417 Processing helix chain 'F' and resid 475 through 482 Processing helix chain 'F' and resid 487 through 501 Processing helix chain 'F' and resid 521 through 531 Processing helix chain 'F' and resid 551 through 554 Processing helix chain 'F' and resid 575 through 582 Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 641 through 645 Processing helix chain 'F' and resid 647 through 649 No H-bonds generated for 'chain 'F' and resid 647 through 649' Processing helix chain 'F' and resid 651 through 663 Processing helix chain 'F' and resid 674 through 686 WARNING: missing atoms! Processing helix chain 'F' and resid 688 through 695 Processing helix chain 'F' and resid 707 through 719 removed outlier: 6.428A pdb=" N PHE F 713 " --> pdb=" O ILE F 709 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N TYR F 714 " --> pdb=" O VAL F 710 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS F 715 " --> pdb=" O TYR F 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 736 Processing helix chain 'D' and resid 317 through 338 Processing helix chain 'D' and resid 350 through 360 Processing helix chain 'D' and resid 388 through 398 Processing helix chain 'D' and resid 404 through 417 Processing helix chain 'D' and resid 475 through 482 Processing helix chain 'D' and resid 487 through 501 Processing helix chain 'D' and resid 521 through 531 Processing helix chain 'D' and resid 551 through 554 Processing helix chain 'D' and resid 575 through 582 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 641 through 645 Processing helix chain 'D' and resid 647 through 649 No H-bonds generated for 'chain 'D' and resid 647 through 649' Processing helix chain 'D' and resid 651 through 663 Processing helix chain 'D' and resid 674 through 686 WARNING: missing atoms! Processing helix chain 'D' and resid 688 through 695 Processing helix chain 'D' and resid 707 through 719 removed outlier: 7.069A pdb=" N PHE D 713 " --> pdb=" O ILE D 709 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR D 714 " --> pdb=" O VAL D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 736 Processing helix chain 'E' and resid 317 through 338 Processing helix chain 'E' and resid 350 through 360 Processing helix chain 'E' and resid 388 through 398 removed outlier: 3.569A pdb=" N LEU E 398 " --> pdb=" O VAL E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 417 Processing helix chain 'E' and resid 475 through 482 Processing helix chain 'E' and resid 487 through 501 removed outlier: 3.548A pdb=" N MET E 501 " --> pdb=" O ILE E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 531 Processing helix chain 'E' and resid 550 through 556 removed outlier: 3.885A pdb=" N VAL E 553 " --> pdb=" O LYS E 550 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY E 556 " --> pdb=" O VAL E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 582 Processing helix chain 'E' and resid 619 through 624 removed outlier: 3.565A pdb=" N ARG E 624 " --> pdb=" O GLY E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 645 Processing helix chain 'E' and resid 647 through 649 No H-bonds generated for 'chain 'E' and resid 647 through 649' Processing helix chain 'E' and resid 651 through 663 Processing helix chain 'E' and resid 674 through 686 WARNING: missing atoms! Processing helix chain 'E' and resid 688 through 694 Processing helix chain 'E' and resid 707 through 719 removed outlier: 6.172A pdb=" N PHE E 713 " --> pdb=" O ILE E 709 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N TYR E 714 " --> pdb=" O VAL E 710 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS E 715 " --> pdb=" O TYR E 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 729 through 736 Processing helix chain 'C' and resid 317 through 338 Processing helix chain 'C' and resid 350 through 360 Processing helix chain 'C' and resid 388 through 398 removed outlier: 3.595A pdb=" N LEU C 398 " --> pdb=" O VAL C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 417 Processing helix chain 'C' and resid 475 through 482 Processing helix chain 'C' and resid 487 through 501 Processing helix chain 'C' and resid 521 through 531 Processing helix chain 'C' and resid 551 through 554 Processing helix chain 'C' and resid 575 through 582 Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.611A pdb=" N ARG C 624 " --> pdb=" O GLY C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 645 Processing helix chain 'C' and resid 647 through 649 No H-bonds generated for 'chain 'C' and resid 647 through 649' Processing helix chain 'C' and resid 651 through 663 Processing helix chain 'C' and resid 674 through 686 WARNING: missing atoms! Processing helix chain 'C' and resid 688 through 694 Processing helix chain 'C' and resid 707 through 719 removed outlier: 6.117A pdb=" N PHE C 713 " --> pdb=" O ILE C 709 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N TYR C 714 " --> pdb=" O VAL C 710 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS C 715 " --> pdb=" O TYR C 711 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 716 " --> pdb=" O ALA C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 736 Processing sheet with id= A, first strand: chain 'A' and resid 363 through 365 Processing sheet with id= B, first strand: chain 'A' and resid 429 through 431 Processing sheet with id= C, first strand: chain 'A' and resid 625 through 628 removed outlier: 5.828A pdb=" N ALA A 510 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL A 628 " --> pdb=" O ALA A 510 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE A 512 " --> pdb=" O VAL A 628 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL A 604 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N PHE A 513 " --> pdb=" O VAL A 604 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLN A 606 " --> pdb=" O PHE A 513 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 586 through 589 removed outlier: 3.582A pdb=" N ALA A 598 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 363 through 365 Processing sheet with id= F, first strand: chain 'B' and resid 429 through 431 Processing sheet with id= G, first strand: chain 'B' and resid 625 through 628 removed outlier: 5.713A pdb=" N ALA B 510 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL B 628 " --> pdb=" O ALA B 510 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE B 512 " --> pdb=" O VAL B 628 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL B 604 " --> pdb=" O ILE B 511 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N PHE B 513 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLN B 606 " --> pdb=" O PHE B 513 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 586 through 589 Processing sheet with id= I, first strand: chain 'F' and resid 363 through 365 Processing sheet with id= J, first strand: chain 'F' and resid 429 through 431 Processing sheet with id= K, first strand: chain 'F' and resid 625 through 628 removed outlier: 5.747A pdb=" N ALA F 510 " --> pdb=" O LEU F 626 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL F 628 " --> pdb=" O ALA F 510 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE F 512 " --> pdb=" O VAL F 628 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL F 604 " --> pdb=" O ILE F 511 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N PHE F 513 " --> pdb=" O VAL F 604 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLN F 606 " --> pdb=" O PHE F 513 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 586 through 588 Processing sheet with id= M, first strand: chain 'D' and resid 363 through 365 Processing sheet with id= N, first strand: chain 'D' and resid 429 through 431 Processing sheet with id= O, first strand: chain 'D' and resid 625 through 628 removed outlier: 5.723A pdb=" N ALA D 510 " --> pdb=" O LEU D 626 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL D 628 " --> pdb=" O ALA D 510 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE D 512 " --> pdb=" O VAL D 628 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL D 604 " --> pdb=" O ILE D 511 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N PHE D 513 " --> pdb=" O VAL D 604 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLN D 606 " --> pdb=" O PHE D 513 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 586 through 589 Processing sheet with id= Q, first strand: chain 'E' and resid 363 through 365 Processing sheet with id= R, first strand: chain 'E' and resid 429 through 431 Processing sheet with id= S, first strand: chain 'E' and resid 625 through 628 removed outlier: 5.788A pdb=" N ALA E 510 " --> pdb=" O LEU E 626 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL E 628 " --> pdb=" O ALA E 510 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE E 512 " --> pdb=" O VAL E 628 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL E 604 " --> pdb=" O ILE E 511 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N PHE E 513 " --> pdb=" O VAL E 604 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN E 606 " --> pdb=" O PHE E 513 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 586 through 588 removed outlier: 3.521A pdb=" N ALA E 598 " --> pdb=" O VAL E 586 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 363 through 365 Processing sheet with id= V, first strand: chain 'C' and resid 429 through 431 Processing sheet with id= W, first strand: chain 'C' and resid 625 through 628 removed outlier: 5.828A pdb=" N ALA C 510 " --> pdb=" O LEU C 626 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL C 628 " --> pdb=" O ALA C 510 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE C 512 " --> pdb=" O VAL C 628 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL C 604 " --> pdb=" O ILE C 511 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N PHE C 513 " --> pdb=" O VAL C 604 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN C 606 " --> pdb=" O PHE C 513 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 586 through 589 removed outlier: 3.591A pdb=" N ALA C 598 " --> pdb=" O VAL C 586 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 2058 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: 6.65 Time building geometry restraints manager: 9.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6153 1.33 - 1.45: 3788 1.45 - 1.57: 12425 1.57 - 1.69: 31 1.69 - 1.81: 113 Bond restraints: 22510 Sorted by residual: bond pdb=" O3A ANP C1201 " pdb=" PB ANP C1201 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" O3A ANP B1201 " pdb=" PB ANP B1201 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.23e+01 bond pdb=" O3A ANP F1201 " pdb=" PB ANP F1201 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" O3A ANP A1201 " pdb=" PB ANP A1201 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" O3A ANP D1201 " pdb=" PB ANP D1201 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.18e+01 ... (remaining 22505 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.65: 495 106.65 - 113.50: 12029 113.50 - 120.34: 8220 120.34 - 127.18: 9476 127.18 - 134.03: 195 Bond angle restraints: 30415 Sorted by residual: angle pdb=" PB ANP C1201 " pdb=" N3B ANP C1201 " pdb=" PG ANP C1201 " ideal model delta sigma weight residual 126.95 109.13 17.82 3.00e+00 1.11e-01 3.53e+01 angle pdb=" PB ANP F1201 " pdb=" N3B ANP F1201 " pdb=" PG ANP F1201 " ideal model delta sigma weight residual 126.95 109.26 17.69 3.00e+00 1.11e-01 3.48e+01 angle pdb=" PB ANP A1201 " pdb=" N3B ANP A1201 " pdb=" PG ANP A1201 " ideal model delta sigma weight residual 126.95 109.30 17.65 3.00e+00 1.11e-01 3.46e+01 angle pdb=" PB ANP B1201 " pdb=" N3B ANP B1201 " pdb=" PG ANP B1201 " ideal model delta sigma weight residual 126.95 109.32 17.63 3.00e+00 1.11e-01 3.45e+01 angle pdb=" PB ANP E1201 " pdb=" N3B ANP E1201 " pdb=" PG ANP E1201 " ideal model delta sigma weight residual 126.95 109.33 17.62 3.00e+00 1.11e-01 3.45e+01 ... (remaining 30410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.19: 13279 33.19 - 66.38: 292 66.38 - 99.57: 56 99.57 - 132.75: 0 132.75 - 165.94: 6 Dihedral angle restraints: 13633 sinusoidal: 5812 harmonic: 7821 Sorted by residual: dihedral pdb=" O1B ANP C1201 " pdb=" N3B ANP C1201 " pdb=" PB ANP C1201 " pdb=" PG ANP C1201 " ideal model delta sinusoidal sigma weight residual 35.15 -130.79 165.94 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" O1B ANP B1201 " pdb=" N3B ANP B1201 " pdb=" PB ANP B1201 " pdb=" PG ANP B1201 " ideal model delta sinusoidal sigma weight residual 35.15 -129.46 164.61 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" O1B ANP E1201 " pdb=" N3B ANP E1201 " pdb=" PB ANP E1201 " pdb=" PG ANP E1201 " ideal model delta sinusoidal sigma weight residual 35.15 -129.25 164.40 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 13630 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2727 0.056 - 0.111: 470 0.111 - 0.167: 57 0.167 - 0.222: 2 0.222 - 0.278: 7 Chirality restraints: 3263 Sorted by residual: chirality pdb=" C3' ANP B1201 " pdb=" C2' ANP B1201 " pdb=" C4' ANP B1201 " pdb=" O3' ANP B1201 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C3' ANP C1201 " pdb=" C2' ANP C1201 " pdb=" C4' ANP C1201 " pdb=" O3' ANP C1201 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C3' ANP A1201 " pdb=" C2' ANP A1201 " pdb=" C4' ANP A1201 " pdb=" O3' ANP A1201 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 3260 not shown) Planarity restraints: 3898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 349 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO D 350 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 350 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 350 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 448 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO B 449 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 449 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 449 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 448 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.66e+00 pdb=" N PRO E 449 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO E 449 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 449 " 0.018 5.00e-02 4.00e+02 ... (remaining 3895 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2137 2.75 - 3.29: 23175 3.29 - 3.82: 36658 3.82 - 4.36: 45312 4.36 - 4.90: 74159 Nonbonded interactions: 181441 Sorted by model distance: nonbonded pdb=" OG SER A 574 " pdb=" OD2 ASP A 616 " model vdw 2.209 2.440 nonbonded pdb=" OE1 GLU E 680 " pdb=" OH TYR E 690 " model vdw 2.210 2.440 nonbonded pdb=" OG SER C 574 " pdb=" OD2 ASP C 616 " model vdw 2.223 2.440 nonbonded pdb=" OG SER F 574 " pdb=" OD2 ASP F 616 " model vdw 2.242 2.440 nonbonded pdb=" OE1 GLU D 547 " pdb=" NZ LYS D 550 " model vdw 2.246 2.520 ... (remaining 181436 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 316 through 750 or resid 754 through 766 or resid 1201)) selection = (chain 'B' and (resid 316 through 750 or resid 754 through 766 or resid 1201)) selection = (chain 'C' and (resid 316 through 750 or resid 754 through 766 or resid 1201)) selection = chain 'D' selection = (chain 'E' and (resid 316 through 750 or resid 754 through 766 or resid 1201)) selection = (chain 'F' and (resid 316 through 750 or resid 754 through 766 or resid 1201)) } 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: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.900 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 57.100 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 22510 Z= 0.274 Angle : 0.633 17.815 30415 Z= 0.324 Chirality : 0.043 0.278 3263 Planarity : 0.003 0.033 3898 Dihedral : 15.336 165.942 8583 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.04 % Allowed : 0.54 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.24 (0.16), residues: 2597 helix: 2.35 (0.16), residues: 1037 sheet: 0.21 (0.33), residues: 250 loop : -0.28 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 335 HIS 0.006 0.001 HIS B 402 PHE 0.021 0.001 PHE B 713 TYR 0.019 0.001 TYR D 711 ARG 0.002 0.000 ARG C 597 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 2.723 Fit side-chains REVERT: A 708 TYR cc_start: 0.8627 (p90) cc_final: 0.8240 (p90) REVERT: A 732 TYR cc_start: 0.7985 (t80) cc_final: 0.7683 (t80) REVERT: B 331 MET cc_start: 0.8724 (mtp) cc_final: 0.8450 (mtp) REVERT: B 737 HIS cc_start: 0.8696 (t70) cc_final: 0.8159 (t70) REVERT: F 690 TYR cc_start: 0.9176 (t80) cc_final: 0.8460 (t80) REVERT: F 737 HIS cc_start: 0.8415 (t70) cc_final: 0.7875 (t70) REVERT: D 737 HIS cc_start: 0.8420 (t70) cc_final: 0.7864 (t70) REVERT: C 331 MET cc_start: 0.8938 (mtp) cc_final: 0.8730 (mtp) REVERT: C 690 TYR cc_start: 0.9119 (t80) cc_final: 0.8539 (t80) REVERT: C 737 HIS cc_start: 0.8463 (t70) cc_final: 0.7995 (t70) outliers start: 1 outliers final: 1 residues processed: 92 average time/residue: 0.3033 time to fit residues: 47.8065 Evaluate side-chains 77 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 595 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 737 HIS D 734 GLN ** C 724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 22510 Z= 0.574 Angle : 0.634 7.261 30415 Z= 0.335 Chirality : 0.047 0.168 3263 Planarity : 0.004 0.054 3898 Dihedral : 12.410 176.757 3061 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.54 % Allowed : 5.76 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 2597 helix: 1.42 (0.15), residues: 1161 sheet: 0.31 (0.36), residues: 215 loop : -0.47 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 335 HIS 0.005 0.001 HIS E 402 PHE 0.015 0.002 PHE B 600 TYR 0.017 0.002 TYR F 461 ARG 0.003 0.001 ARG D 624 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 2.570 Fit side-chains REVERT: A 708 TYR cc_start: 0.8480 (p90) cc_final: 0.8137 (p90) REVERT: B 737 HIS cc_start: 0.8649 (t70) cc_final: 0.7728 (t70) REVERT: F 690 TYR cc_start: 0.9124 (t80) cc_final: 0.8473 (t80) REVERT: F 737 HIS cc_start: 0.8286 (t-90) cc_final: 0.7704 (t70) REVERT: D 737 HIS cc_start: 0.8451 (t70) cc_final: 0.7686 (t70) REVERT: E 690 TYR cc_start: 0.8777 (t80) cc_final: 0.8346 (t80) REVERT: E 713 PHE cc_start: 0.9061 (t80) cc_final: 0.8770 (t80) REVERT: C 690 TYR cc_start: 0.9128 (t80) cc_final: 0.8548 (t80) REVERT: C 737 HIS cc_start: 0.8508 (t70) cc_final: 0.7876 (t70) outliers start: 13 outliers final: 4 residues processed: 85 average time/residue: 0.2862 time to fit residues: 42.5095 Evaluate side-chains 83 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain E residue 678 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 199 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 259 optimal weight: 1.9990 chunk 213 optimal weight: 0.2980 chunk 238 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 192 optimal weight: 0.7980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 ASN D 471 ASN E 358 ASN C 358 ASN C 724 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22510 Z= 0.187 Angle : 0.435 7.077 30415 Z= 0.236 Chirality : 0.041 0.188 3263 Planarity : 0.003 0.048 3898 Dihedral : 10.636 168.374 3061 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.78 % Allowed : 7.20 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.05 (0.16), residues: 2597 helix: 2.10 (0.16), residues: 1082 sheet: 0.12 (0.35), residues: 225 loop : -0.40 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 335 HIS 0.003 0.001 HIS E 402 PHE 0.015 0.001 PHE C 735 TYR 0.025 0.001 TYR D 711 ARG 0.001 0.000 ARG C 703 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 2.692 Fit side-chains REVERT: A 708 TYR cc_start: 0.8466 (p90) cc_final: 0.8141 (p90) REVERT: B 737 HIS cc_start: 0.8678 (t70) cc_final: 0.8101 (t70) REVERT: F 690 TYR cc_start: 0.9099 (t80) cc_final: 0.8381 (t80) REVERT: F 737 HIS cc_start: 0.8299 (t-90) cc_final: 0.7657 (t70) REVERT: D 732 TYR cc_start: 0.7750 (t80) cc_final: 0.7418 (t80) REVERT: D 737 HIS cc_start: 0.8459 (t70) cc_final: 0.7725 (t70) REVERT: E 732 TYR cc_start: 0.7611 (t80) cc_final: 0.7252 (t80) REVERT: C 690 TYR cc_start: 0.9069 (t80) cc_final: 0.8472 (t80) REVERT: C 737 HIS cc_start: 0.8492 (t70) cc_final: 0.7817 (t70) outliers start: 19 outliers final: 6 residues processed: 84 average time/residue: 0.3040 time to fit residues: 44.4320 Evaluate side-chains 83 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain E residue 731 PHE Chi-restraints excluded: chain C residue 731 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 241 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 228 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 471 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 22510 Z= 0.416 Angle : 0.526 7.706 30415 Z= 0.283 Chirality : 0.043 0.167 3263 Planarity : 0.003 0.050 3898 Dihedral : 10.535 170.245 3061 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.70 % Allowed : 8.73 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.16), residues: 2597 helix: 1.82 (0.16), residues: 1113 sheet: 0.01 (0.34), residues: 225 loop : -0.50 (0.16), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 335 HIS 0.003 0.001 HIS E 402 PHE 0.011 0.001 PHE C 682 TYR 0.022 0.001 TYR B 717 ARG 0.002 0.000 ARG D 507 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 2.690 Fit side-chains REVERT: A 708 TYR cc_start: 0.8536 (p90) cc_final: 0.8198 (p90) REVERT: B 737 HIS cc_start: 0.8679 (t70) cc_final: 0.7710 (t70) REVERT: F 690 TYR cc_start: 0.9095 (t80) cc_final: 0.8422 (t80) REVERT: F 713 PHE cc_start: 0.9190 (t80) cc_final: 0.8872 (t80) REVERT: F 737 HIS cc_start: 0.8292 (t-90) cc_final: 0.7920 (t70) REVERT: D 732 TYR cc_start: 0.7794 (t80) cc_final: 0.7457 (t80) REVERT: D 737 HIS cc_start: 0.8452 (t70) cc_final: 0.7677 (t70) REVERT: E 732 TYR cc_start: 0.7638 (t80) cc_final: 0.7352 (t80) REVERT: C 690 TYR cc_start: 0.9092 (t80) cc_final: 0.8515 (t80) REVERT: C 737 HIS cc_start: 0.8474 (t70) cc_final: 0.7720 (t70) outliers start: 17 outliers final: 7 residues processed: 81 average time/residue: 0.3035 time to fit residues: 43.0473 Evaluate side-chains 83 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain F residue 542 VAL Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain E residue 731 PHE Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 731 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 190 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 217 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 130 optimal weight: 30.0000 chunk 229 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22510 Z= 0.224 Angle : 0.447 8.754 30415 Z= 0.241 Chirality : 0.041 0.155 3263 Planarity : 0.003 0.052 3898 Dihedral : 10.198 165.942 3059 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.82 % Allowed : 9.43 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.16), residues: 2597 helix: 2.07 (0.16), residues: 1082 sheet: 0.02 (0.33), residues: 225 loop : -0.44 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 335 HIS 0.002 0.001 HIS E 402 PHE 0.006 0.001 PHE A 682 TYR 0.020 0.001 TYR D 711 ARG 0.001 0.000 ARG F 703 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 708 TYR cc_start: 0.8491 (p90) cc_final: 0.8163 (p90) REVERT: B 708 TYR cc_start: 0.8467 (p90) cc_final: 0.8128 (p90) REVERT: B 737 HIS cc_start: 0.8675 (t70) cc_final: 0.8323 (t70) REVERT: F 690 TYR cc_start: 0.9066 (t80) cc_final: 0.8386 (t80) REVERT: F 713 PHE cc_start: 0.9194 (t80) cc_final: 0.8884 (t80) REVERT: F 737 HIS cc_start: 0.8258 (t-90) cc_final: 0.7853 (t70) REVERT: D 732 TYR cc_start: 0.7740 (t80) cc_final: 0.7440 (t80) REVERT: D 737 HIS cc_start: 0.8446 (t70) cc_final: 0.7579 (t70) REVERT: C 690 TYR cc_start: 0.9076 (t80) cc_final: 0.8461 (t80) REVERT: C 737 HIS cc_start: 0.8505 (t70) cc_final: 0.8246 (t70) outliers start: 20 outliers final: 12 residues processed: 87 average time/residue: 0.2754 time to fit residues: 42.3898 Evaluate side-chains 90 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain F residue 542 VAL Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 731 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 5.9990 chunk 229 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 255 optimal weight: 0.7980 chunk 212 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22510 Z= 0.170 Angle : 0.423 9.330 30415 Z= 0.228 Chirality : 0.040 0.154 3263 Planarity : 0.003 0.050 3898 Dihedral : 9.941 165.218 3059 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.70 % Allowed : 9.92 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.13 (0.16), residues: 2597 helix: 2.24 (0.16), residues: 1080 sheet: 0.09 (0.34), residues: 225 loop : -0.42 (0.16), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 335 HIS 0.002 0.000 HIS E 402 PHE 0.008 0.001 PHE E 713 TYR 0.013 0.001 TYR F 717 ARG 0.001 0.000 ARG F 703 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 2.374 Fit side-chains revert: symmetry clash REVERT: A 516 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8131 (p0) REVERT: A 708 TYR cc_start: 0.8470 (p90) cc_final: 0.8129 (p90) REVERT: F 690 TYR cc_start: 0.9054 (t80) cc_final: 0.8311 (t80) REVERT: F 713 PHE cc_start: 0.9193 (t80) cc_final: 0.8888 (t80) REVERT: D 737 HIS cc_start: 0.8401 (t70) cc_final: 0.7601 (t70) REVERT: E 713 PHE cc_start: 0.9075 (t80) cc_final: 0.8787 (t80) REVERT: C 690 TYR cc_start: 0.9074 (t80) cc_final: 0.8440 (t80) REVERT: C 737 HIS cc_start: 0.8499 (t70) cc_final: 0.7747 (t70) outliers start: 17 outliers final: 9 residues processed: 89 average time/residue: 0.3082 time to fit residues: 47.5020 Evaluate side-chains 87 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain F residue 542 VAL Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 678 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 254 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 155 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 22510 Z= 0.122 Angle : 0.407 10.178 30415 Z= 0.219 Chirality : 0.040 0.154 3263 Planarity : 0.003 0.054 3898 Dihedral : 9.719 163.850 3059 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.49 % Allowed : 10.33 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.25 (0.17), residues: 2597 helix: 2.35 (0.16), residues: 1082 sheet: 0.19 (0.34), residues: 225 loop : -0.37 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP E 335 HIS 0.003 0.000 HIS E 402 PHE 0.005 0.001 PHE A 363 TYR 0.038 0.001 TYR D 711 ARG 0.001 0.000 ARG F 703 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 2.732 Fit side-chains revert: symmetry clash REVERT: A 708 TYR cc_start: 0.8435 (p90) cc_final: 0.8107 (p90) REVERT: F 690 TYR cc_start: 0.9032 (t80) cc_final: 0.8436 (t80) REVERT: F 737 HIS cc_start: 0.8202 (t70) cc_final: 0.7927 (m90) REVERT: D 737 HIS cc_start: 0.8412 (t70) cc_final: 0.7619 (t70) REVERT: E 713 PHE cc_start: 0.9098 (t80) cc_final: 0.8872 (t80) REVERT: C 690 TYR cc_start: 0.9028 (t80) cc_final: 0.8397 (t80) REVERT: C 737 HIS cc_start: 0.8467 (t70) cc_final: 0.7734 (t70) outliers start: 12 outliers final: 8 residues processed: 89 average time/residue: 0.2896 time to fit residues: 45.5367 Evaluate side-chains 85 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain F residue 542 VAL Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain C residue 678 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 4.9990 chunk 101 optimal weight: 0.3980 chunk 151 optimal weight: 8.9990 chunk 76 optimal weight: 0.0970 chunk 49 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22510 Z= 0.137 Angle : 0.410 10.055 30415 Z= 0.221 Chirality : 0.040 0.153 3263 Planarity : 0.003 0.051 3898 Dihedral : 9.656 164.187 3059 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.49 % Allowed : 10.75 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2597 helix: 2.38 (0.16), residues: 1082 sheet: 0.21 (0.34), residues: 227 loop : -0.36 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP E 335 HIS 0.002 0.000 HIS E 402 PHE 0.014 0.001 PHE F 713 TYR 0.033 0.001 TYR D 711 ARG 0.001 0.000 ARG D 507 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 2.515 Fit side-chains revert: symmetry clash REVERT: A 708 TYR cc_start: 0.8423 (p90) cc_final: 0.8090 (p90) REVERT: B 737 HIS cc_start: 0.8787 (t70) cc_final: 0.8356 (t70) REVERT: F 690 TYR cc_start: 0.9028 (t80) cc_final: 0.8292 (t80) REVERT: D 737 HIS cc_start: 0.8419 (t70) cc_final: 0.7632 (t70) REVERT: C 690 TYR cc_start: 0.9014 (t80) cc_final: 0.8367 (t80) REVERT: C 737 HIS cc_start: 0.8445 (t70) cc_final: 0.7703 (t70) outliers start: 12 outliers final: 8 residues processed: 81 average time/residue: 0.2926 time to fit residues: 41.6377 Evaluate side-chains 84 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain F residue 542 VAL Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 678 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 5.9990 chunk 222 optimal weight: 0.0050 chunk 237 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 186 optimal weight: 0.4980 chunk 72 optimal weight: 9.9990 chunk 214 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 236 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 overall best weight: 1.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 737 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22510 Z= 0.166 Angle : 0.421 10.546 30415 Z= 0.227 Chirality : 0.040 0.163 3263 Planarity : 0.003 0.049 3898 Dihedral : 9.627 163.556 3059 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.45 % Allowed : 11.12 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2597 helix: 2.41 (0.16), residues: 1077 sheet: 0.24 (0.35), residues: 227 loop : -0.38 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 335 HIS 0.002 0.000 HIS E 402 PHE 0.017 0.001 PHE E 713 TYR 0.032 0.001 TYR D 711 ARG 0.001 0.000 ARG E 623 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 2.463 Fit side-chains REVERT: A 708 TYR cc_start: 0.8431 (p90) cc_final: 0.8103 (p90) REVERT: B 737 HIS cc_start: 0.8786 (t70) cc_final: 0.8351 (t70) REVERT: F 690 TYR cc_start: 0.9020 (t80) cc_final: 0.8359 (t80) REVERT: F 737 HIS cc_start: 0.8348 (t-170) cc_final: 0.7997 (t70) REVERT: D 737 HIS cc_start: 0.8419 (t70) cc_final: 0.7620 (t70) REVERT: C 690 TYR cc_start: 0.9002 (t80) cc_final: 0.8383 (t80) REVERT: C 737 HIS cc_start: 0.8447 (t70) cc_final: 0.7683 (t70) outliers start: 11 outliers final: 7 residues processed: 79 average time/residue: 0.2937 time to fit residues: 40.9275 Evaluate side-chains 80 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain F residue 542 VAL Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 678 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 174 optimal weight: 8.9990 chunk 263 optimal weight: 40.0000 chunk 242 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 161 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 166 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 724 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22510 Z= 0.160 Angle : 0.426 11.049 30415 Z= 0.230 Chirality : 0.040 0.180 3263 Planarity : 0.003 0.049 3898 Dihedral : 9.557 162.234 3059 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.37 % Allowed : 11.28 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2597 helix: 2.40 (0.16), residues: 1077 sheet: 0.25 (0.35), residues: 227 loop : -0.37 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP E 335 HIS 0.002 0.000 HIS E 402 PHE 0.012 0.001 PHE F 713 TYR 0.033 0.001 TYR D 711 ARG 0.001 0.000 ARG E 623 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 2.579 Fit side-chains REVERT: A 708 TYR cc_start: 0.8426 (p90) cc_final: 0.8073 (p90) REVERT: B 737 HIS cc_start: 0.8762 (t70) cc_final: 0.8172 (t70) REVERT: F 690 TYR cc_start: 0.9009 (t80) cc_final: 0.8343 (t80) REVERT: C 690 TYR cc_start: 0.9000 (t80) cc_final: 0.8361 (t80) REVERT: C 737 HIS cc_start: 0.8447 (t70) cc_final: 0.7679 (t70) outliers start: 9 outliers final: 8 residues processed: 77 average time/residue: 0.2895 time to fit residues: 39.5791 Evaluate side-chains 79 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain F residue 542 VAL Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 678 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 87 optimal weight: 40.0000 chunk 215 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 184 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.082067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.054338 restraints weight = 82164.804| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.42 r_work: 0.2830 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22510 Z= 0.256 Angle : 0.457 10.915 30415 Z= 0.246 Chirality : 0.041 0.151 3263 Planarity : 0.003 0.048 3898 Dihedral : 9.609 161.763 3059 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.45 % Allowed : 11.32 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2597 helix: 2.18 (0.16), residues: 1107 sheet: 0.56 (0.36), residues: 212 loop : -0.39 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 335 HIS 0.002 0.001 HIS E 402 PHE 0.011 0.001 PHE F 713 TYR 0.032 0.001 TYR D 711 ARG 0.001 0.000 ARG C 507 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3491.58 seconds wall clock time: 65 minutes 32.31 seconds (3932.31 seconds total)