Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 04:33:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7om0_12982/04_2023/7om0_12982_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7om0_12982/04_2023/7om0_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_12982/04_2023/7om0_12982.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7om0_12982/04_2023/7om0_12982.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7om0_12982/04_2023/7om0_12982_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7om0_12982/04_2023/7om0_12982_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 10.29, per 1000 atoms: 0.47 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: 8.87 Conformation dependent library (CDL) restraints added in 3.0 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: 2.70 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: 6.19 Time building geometry restraints manager: 9.49 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: 13231 33.19 - 66.38: 214 66.38 - 99.57: 14 99.57 - 132.75: 0 132.75 - 165.94: 6 Dihedral angle restraints: 13465 sinusoidal: 5644 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 13462 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: 3.610 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: 11.750 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 51.400 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.140 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.780 ------------------------------------------------------------------------------- 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 : 13.266 165.942 8415 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 % 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 *********************** 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 : 2.802 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 92 average time/residue: 0.3145 time to fit residues: 50.2229 Evaluate side-chains 77 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 2.708 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1897 time to fit residues: 4.0659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 154 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 734 GLN 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: 0.8548 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.063 22510 Z= 0.629 Angle : 0.654 7.621 30415 Z= 0.351 Chirality : 0.046 0.171 3263 Planarity : 0.004 0.054 3898 Dihedral : 9.409 176.305 2891 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.49 % 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: 0.57 (0.16), residues: 2597 helix: 1.32 (0.15), residues: 1161 sheet: 0.28 (0.36), residues: 215 loop : -0.48 (0.16), residues: 1221 *********************** 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 93 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 2.749 Fit side-chains outliers start: 12 outliers final: 3 residues processed: 83 average time/residue: 0.3062 time to fit residues: 44.5507 Evaluate side-chains 82 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 2.772 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2230 time to fit residues: 4.9625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 240 optimal weight: 4.9990 chunk 259 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 chunk 238 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 192 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 ASN B 734 GLN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 ASN E 358 ASN C 358 ASN C 724 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 22510 Z= 0.284 Angle : 0.469 6.846 30415 Z= 0.256 Chirality : 0.041 0.165 3263 Planarity : 0.003 0.051 3898 Dihedral : 9.094 170.641 2891 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.70 % 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: 0.86 (0.16), residues: 2597 helix: 1.82 (0.16), residues: 1092 sheet: 0.03 (0.34), residues: 225 loop : -0.40 (0.16), residues: 1280 *********************** 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 95 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 2.919 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 82 average time/residue: 0.3057 time to fit residues: 44.3782 Evaluate side-chains 83 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 2.541 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2234 time to fit residues: 6.3306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 241 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 chunk 228 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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: 0.8487 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 22510 Z= 0.258 Angle : 0.452 7.913 30415 Z= 0.246 Chirality : 0.041 0.159 3263 Planarity : 0.003 0.051 3898 Dihedral : 8.969 169.409 2891 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 0.58 % 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: 0.90 (0.16), residues: 2597 helix: 1.95 (0.16), residues: 1082 sheet: -0.02 (0.34), residues: 225 loop : -0.44 (0.16), residues: 1290 *********************** 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 89 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 2.735 Fit side-chains outliers start: 14 outliers final: 2 residues processed: 80 average time/residue: 0.3088 time to fit residues: 43.4817 Evaluate side-chains 75 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 2.889 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2179 time to fit residues: 4.7488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 3 optimal weight: 0.8980 chunk 190 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 217 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 229 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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: 0.8488 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 22510 Z= 0.262 Angle : 0.458 9.215 30415 Z= 0.248 Chirality : 0.041 0.172 3263 Planarity : 0.003 0.049 3898 Dihedral : 8.918 168.321 2891 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 0.66 % 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: 0.86 (0.16), residues: 2597 helix: 1.87 (0.16), residues: 1112 sheet: 0.01 (0.33), residues: 225 loop : -0.49 (0.16), residues: 1260 *********************** 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 92 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 2.681 Fit side-chains outliers start: 16 outliers final: 5 residues processed: 82 average time/residue: 0.3064 time to fit residues: 44.6854 Evaluate side-chains 80 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 2.822 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2298 time to fit residues: 6.1064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 4.9990 chunk 229 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 255 optimal weight: 10.0000 chunk 212 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- 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: 0.8480 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 22510 Z= 0.235 Angle : 0.448 9.026 30415 Z= 0.244 Chirality : 0.041 0.153 3263 Planarity : 0.003 0.052 3898 Dihedral : 8.833 167.060 2891 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.70 % 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: 0.95 (0.16), residues: 2597 helix: 2.06 (0.16), residues: 1075 sheet: 0.05 (0.33), residues: 225 loop : -0.47 (0.16), residues: 1297 *********************** 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 92 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 83 average time/residue: 0.3105 time to fit residues: 45.3061 Evaluate side-chains 83 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 2.692 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2143 time to fit residues: 6.6266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 145 optimal weight: 0.0770 chunk 186 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 254 optimal weight: 0.8980 chunk 159 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 overall best weight: 1.1540 ------------------------------------------------------------------------------- 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: 0.8446 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 22510 Z= 0.145 Angle : 0.419 9.845 30415 Z= 0.228 Chirality : 0.040 0.181 3263 Planarity : 0.003 0.053 3898 Dihedral : 8.693 166.499 2891 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 0.33 % 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: 1.09 (0.16), residues: 2597 helix: 2.13 (0.16), residues: 1086 sheet: 0.12 (0.34), residues: 225 loop : -0.38 (0.16), residues: 1286 *********************** 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 84 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 2.879 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 80 average time/residue: 0.3098 time to fit residues: 43.1972 Evaluate side-chains 75 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 2.725 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1980 time to fit residues: 4.4642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 6.9990 chunk 101 optimal weight: 0.0020 chunk 151 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 49 optimal weight: 0.1980 chunk 161 optimal weight: 0.9980 chunk 173 optimal weight: 9.9990 chunk 125 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 231 optimal weight: 6.9990 overall best weight: 2.0392 ------------------------------------------------------------------------------- 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: 0.8469 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 22510 Z= 0.216 Angle : 0.437 10.532 30415 Z= 0.236 Chirality : 0.040 0.158 3263 Planarity : 0.003 0.052 3898 Dihedral : 8.715 167.432 2891 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 0.21 % 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: 1.10 (0.16), residues: 2597 helix: 2.14 (0.16), residues: 1083 sheet: 0.16 (0.34), residues: 225 loop : -0.38 (0.16), residues: 1289 *********************** 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 79 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 2.869 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 75 average time/residue: 0.3175 time to fit residues: 41.8218 Evaluate side-chains 73 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 2.645 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2265 time to fit residues: 4.0435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.6980 chunk 222 optimal weight: 5.9990 chunk 237 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 186 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 214 optimal weight: 30.0000 chunk 224 optimal weight: 3.9990 chunk 236 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.8432 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 22510 Z= 0.129 Angle : 0.412 10.965 30415 Z= 0.222 Chirality : 0.040 0.154 3263 Planarity : 0.003 0.052 3898 Dihedral : 8.584 166.204 2891 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.12 % 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: 1.17 (0.16), residues: 2597 helix: 2.21 (0.16), residues: 1083 sheet: 0.21 (0.34), residues: 227 loop : -0.35 (0.16), residues: 1287 *********************** 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 78 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 2.464 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 76 average time/residue: 0.3126 time to fit residues: 41.9588 Evaluate side-chains 73 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 2.616 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2000 time to fit residues: 3.8905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 263 optimal weight: 40.0000 chunk 242 optimal weight: 0.5980 chunk 209 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 161 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 22510 Z= 0.364 Angle : 0.508 10.780 30415 Z= 0.274 Chirality : 0.042 0.150 3263 Planarity : 0.003 0.052 3898 Dihedral : 8.762 167.904 2891 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer Outliers : 0.04 % 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: 0.98 (0.16), residues: 2597 helix: 1.83 (0.16), residues: 1115 sheet: 0.55 (0.36), residues: 210 loop : -0.38 (0.16), residues: 1272 ********************** 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 75 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 2.788 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.3111 time to fit residues: 41.1087 Evaluate side-chains 72 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 2.632 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 87 optimal weight: 40.0000 chunk 215 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.082032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.054137 restraints weight = 81921.260| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.42 r_work: 0.2823 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 22510 Z= 0.262 Angle : 0.469 11.376 30415 Z= 0.255 Chirality : 0.041 0.151 3263 Planarity : 0.003 0.052 3898 Dihedral : 8.640 165.158 2891 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 0.08 % 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: 1.95 (0.16), residues: 1102 sheet: 0.45 (0.35), residues: 212 loop : -0.44 (0.16), residues: 1283 =============================================================================== Job complete usr+sys time: 3443.82 seconds wall clock time: 64 minutes 58.37 seconds (3898.37 seconds total)