Starting phenix.real_space_refine on Sat Sep 12 16:54:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5ken_8242/09_2026/5ken_8242.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ken_8242/09_2026/5ken_8242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5ken_8242/09_2026/5ken_8242.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5ken_8242/09_2026/5ken_8242.cif" model { file = "/net/cci-nas-00/data/ceres_data/5ken_8242/09_2026/5ken_8242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ken_8242/09_2026/5ken_8242.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5ken_8242/09_2026/5ken_8242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ken_8242/09_2026/5ken_8242.map" } resolution = 4.3 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 71 5.16 5 C 10701 2.51 5 N 2796 2.21 5 O 3345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16913 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1596 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 890 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "C" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 903 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "D" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "E" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1829 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 890 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "G" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 903 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "H" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "I" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "J" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 930 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "K" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1829 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "M" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 890 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "N" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 903 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "O" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "P" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "Q" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 930 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.92, per 1000 atoms: 0.23 Number of scatterers: 16913 At special positions: 0 Unit cell: (154.58, 141.48, 149.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 71 16.00 O 3345 8.00 N 2796 7.00 C 10701 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS B 609 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.02 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.02 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.05 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.06 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS F 609 " distance=2.06 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.02 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.02 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.09 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.07 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.07 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.08 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS M 609 " distance=2.04 Simple disulfide: pdb=" SG CYS K 108 " - pdb=" SG CYS K 135 " distance=2.02 Simple disulfide: pdb=" SG CYS K 121 " - pdb=" SG CYS K 147 " distance=2.02 Simple disulfide: pdb=" SG CYS M 511 " - pdb=" SG CYS M 556 " distance=2.04 Simple disulfide: pdb=" SG CYS M 601 " - pdb=" SG CYS M 608 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.02 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.10 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.12 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM16827 O5 NAG U 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-3 " BMA L 3 " - " MAN L 4 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " ALPHA1-6 " BMA L 3 " - " MAN L 5 " " BMA S 3 " - " MAN S 5 " " BMA T 3 " - " MAN T 5 " BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG E 401 " - " ASN E 238 " " NAG K 407 " - " ASN K 238 " " NAG S 1 " - " ASN F 563 " " NAG T 1 " - " ASN M 563 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 804.7 milliseconds 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3884 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 35 sheets defined 16.9% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 85 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'B' and resid 527 through 532 removed outlier: 3.593A pdb=" N TRP B 531 " --> pdb=" O ILE B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 536 Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 553 through 576 removed outlier: 3.518A pdb=" N GLY B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 597 Processing helix chain 'C' and resid 26 through 32 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 83 through 86 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 78 through 85 Processing helix chain 'E' and resid 210 through 215 Processing helix chain 'E' and resid 249 through 255 Processing helix chain 'E' and resid 256 through 260 Processing helix chain 'F' and resid 527 through 532 removed outlier: 3.549A pdb=" N TRP F 531 " --> pdb=" O ILE F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 553 through 576 removed outlier: 3.517A pdb=" N GLY F 557 " --> pdb=" O GLY F 553 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 597 Processing helix chain 'G' and resid 26 through 32 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 86 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'J' and resid 40 through 43 Processing helix chain 'J' and resid 60 through 65 removed outlier: 4.290A pdb=" N SER J 65 " --> pdb=" O PRO J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 59 through 61 No H-bonds generated for 'chain 'K' and resid 59 through 61' Processing helix chain 'K' and resid 71 through 74 Processing helix chain 'K' and resid 78 through 85 Processing helix chain 'K' and resid 210 through 215 Processing helix chain 'K' and resid 249 through 256 Processing helix chain 'K' and resid 257 through 260 Processing helix chain 'M' and resid 527 through 532 removed outlier: 3.595A pdb=" N TRP M 531 " --> pdb=" O ILE M 527 " (cutoff:3.500A) Processing helix chain 'M' and resid 533 through 536 Processing helix chain 'M' and resid 538 through 543 removed outlier: 3.705A pdb=" N ILE M 542 " --> pdb=" O ALA M 539 " (cutoff:3.500A) Processing helix chain 'M' and resid 553 through 576 removed outlier: 3.555A pdb=" N GLY M 557 " --> pdb=" O GLY M 553 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN M 567 " --> pdb=" O ASN M 563 " (cutoff:3.500A) Processing helix chain 'M' and resid 584 through 597 Processing helix chain 'N' and resid 26 through 32 removed outlier: 3.573A pdb=" N PHE N 29 " --> pdb=" O GLY N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 75 No H-bonds generated for 'chain 'N' and resid 73 through 75' Processing helix chain 'N' and resid 83 through 86 Processing helix chain 'O' and resid 79 through 83 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'Q' and resid 40 through 43 Processing helix chain 'Q' and resid 60 through 65 removed outlier: 4.357A pdb=" N SER Q 65 " --> pdb=" O PRO Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 73 through 75 No H-bonds generated for 'chain 'Q' and resid 73 through 75' Processing helix chain 'Q' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.890A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 removed outlier: 4.053A pdb=" N GLU A 103 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 111 removed outlier: 8.393A pdb=" N ALA A 105 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL A 138 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ASN A 107 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N LYS A 140 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N TYR A 109 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N SER A 142 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N LEU A 111 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 10.485A pdb=" N THR A 144 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.209A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.227A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 42 through 45 removed outlier: 6.838A pdb=" N GLY E 36 " --> pdb=" O ILE E 185 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 67 through 69 Processing sheet with id=AB1, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AB2, first strand: chain 'E' and resid 105 through 111 removed outlier: 6.516A pdb=" N GLU E 106 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS E 139 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N CYS E 108 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL E 141 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN E 110 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N GLY E 143 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N TYR E 220 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LYS E 140 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA E 222 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER E 142 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ARG E 219 " --> pdb=" O GLU E 235 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AB4, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.131A pdb=" N GLU G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.324A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.396A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.111A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TYR I 49 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 4 through 8 removed outlier: 5.097A pdb=" N GLY J 16 " --> pdb=" O ASN J 82B" (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 56 through 59 removed outlier: 5.385A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 56 through 59 removed outlier: 5.385A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 42 through 45 removed outlier: 6.573A pdb=" N GLY K 36 " --> pdb=" O ILE K 185 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 67 through 69 Processing sheet with id=AC6, first strand: chain 'K' and resid 102 through 103 Processing sheet with id=AC7, first strand: chain 'K' and resid 107 through 111 removed outlier: 6.499A pdb=" N CYS K 108 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL K 141 " --> pdb=" O CYS K 108 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN K 110 " --> pdb=" O VAL K 141 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N GLY K 143 " --> pdb=" O ASN K 110 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N TYR K 220 " --> pdb=" O VAL K 138 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LYS K 140 " --> pdb=" O TYR K 220 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ALA K 222 " --> pdb=" O LYS K 140 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER K 142 " --> pdb=" O ALA K 222 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ARG K 219 " --> pdb=" O GLU K 235 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 4 through 5 Processing sheet with id=AC9, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.370A pdb=" N GLU N 10 " --> pdb=" O THR N 110 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'O' and resid 10 through 13 removed outlier: 5.908A pdb=" N LEU O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.780A pdb=" N VAL P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR P 49 " --> pdb=" O VAL P 33 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 10 through 13 removed outlier: 4.224A pdb=" N THR P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 4 through 7 removed outlier: 5.462A pdb=" N GLY Q 16 " --> pdb=" O ASN Q 82B" (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 56 through 59 removed outlier: 5.269A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 56 through 59 removed outlier: 5.269A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1407 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.17 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3906 1.32 - 1.45: 4815 1.45 - 1.57: 8489 1.57 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 17302 Sorted by residual: bond pdb=" CA LEU F 569 " pdb=" C LEU F 569 " ideal model delta sigma weight residual 1.524 1.469 0.055 1.26e-02 6.30e+03 1.89e+01 bond pdb=" CA LEU F 515 " pdb=" C LEU F 515 " ideal model delta sigma weight residual 1.526 1.476 0.050 1.20e-02 6.94e+03 1.73e+01 bond pdb=" CA LEU M 569 " pdb=" C LEU M 569 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.26e-02 6.30e+03 1.69e+01 bond pdb=" CA ILE K 301 " pdb=" C ILE K 301 " ideal model delta sigma weight residual 1.524 1.473 0.051 1.30e-02 5.92e+03 1.54e+01 bond pdb=" CA LEU B 569 " pdb=" C LEU B 569 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.27e-02 6.20e+03 1.54e+01 ... (remaining 17297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 19413 2.18 - 4.36: 3188 4.36 - 6.54: 703 6.54 - 8.72: 150 8.72 - 10.90: 29 Bond angle restraints: 23483 Sorted by residual: angle pdb=" C ALA E 125 " pdb=" N PRO E 126 " pdb=" CA PRO E 126 " ideal model delta sigma weight residual 120.03 129.90 -9.87 9.90e-01 1.02e+00 9.95e+01 angle pdb=" C PRO A 93 " pdb=" N PRO A 94 " pdb=" CA PRO A 94 " ideal model delta sigma weight residual 119.85 129.62 -9.77 1.01e+00 9.80e-01 9.36e+01 angle pdb=" C ALA K 125 " pdb=" N PRO K 126 " pdb=" CA PRO K 126 " ideal model delta sigma weight residual 120.03 129.43 -9.40 9.90e-01 1.02e+00 9.02e+01 angle pdb=" C ALA A 125 " pdb=" N PRO A 126 " pdb=" CA PRO A 126 " ideal model delta sigma weight residual 120.03 129.38 -9.35 9.90e-01 1.02e+00 8.92e+01 angle pdb=" C PRO K 93 " pdb=" N PRO K 94 " pdb=" CA PRO K 94 " ideal model delta sigma weight residual 119.85 129.34 -9.49 1.01e+00 9.80e-01 8.84e+01 ... (remaining 23478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 9590 17.91 - 35.83: 265 35.83 - 53.74: 80 53.74 - 71.66: 45 71.66 - 89.57: 29 Dihedral angle restraints: 10009 sinusoidal: 3898 harmonic: 6111 Sorted by residual: dihedral pdb=" CB CYS E 53 " pdb=" SG CYS E 53 " pdb=" SG CYS F 609 " pdb=" CB CYS F 609 " ideal model delta sinusoidal sigma weight residual -86.00 -170.44 84.44 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CA MET J 100D" pdb=" C MET J 100D" pdb=" N GLY J 101 " pdb=" CA GLY J 101 " ideal model delta harmonic sigma weight residual 0.00 44.34 -44.34 0 5.00e+00 4.00e-02 7.86e+01 dihedral pdb=" CB CYS M 601 " pdb=" SG CYS M 601 " pdb=" SG CYS M 608 " pdb=" CB CYS M 608 " ideal model delta sinusoidal sigma weight residual 93.00 168.96 -75.96 1 1.00e+01 1.00e-02 7.27e+01 ... (remaining 10006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.445: 2633 1.445 - 2.890: 0 2.890 - 4.335: 0 4.335 - 5.780: 1 5.780 - 7.226: 1 Chirality restraints: 2635 Sorted by residual: chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN M 563 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 4.83 -7.23 2.00e-01 2.50e+01 1.31e+03 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN F 563 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 2.67 -5.07 2.00e-01 2.50e+01 6.42e+02 chirality pdb=" C1 BMA S 3 " pdb=" O4 NAG S 2 " pdb=" C2 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.42e+01 ... (remaining 2632 not shown) Planarity restraints: 2991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN M 563 " 0.372 2.00e-02 2.50e+03 5.32e-01 3.53e+03 pdb=" CG ASN M 563 " -0.188 2.00e-02 2.50e+03 pdb=" OD1 ASN M 563 " -0.940 2.00e-02 2.50e+03 pdb=" ND2 ASN M 563 " 0.188 2.00e-02 2.50e+03 pdb=" C1 NAG T 1 " 0.568 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 238 " 0.252 2.00e-02 2.50e+03 3.93e-01 1.93e+03 pdb=" CG ASN E 238 " -0.168 2.00e-02 2.50e+03 pdb=" OD1 ASN E 238 " -0.599 2.00e-02 2.50e+03 pdb=" ND2 ASN E 238 " -0.049 2.00e-02 2.50e+03 pdb=" C1 NAG E 401 " 0.565 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 563 " 0.263 2.00e-02 2.50e+03 3.33e-01 1.39e+03 pdb=" CG ASN F 563 " -0.151 2.00e-02 2.50e+03 pdb=" OD1 ASN F 563 " -0.453 2.00e-02 2.50e+03 pdb=" ND2 ASN F 563 " -0.145 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " 0.486 2.00e-02 2.50e+03 ... (remaining 2988 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.01: 11 2.01 - 2.73: 2275 2.73 - 3.45: 24857 3.45 - 4.18: 45430 4.18 - 4.90: 76778 Nonbonded interactions: 149351 Sorted by model distance: nonbonded pdb=" OE1 GLU K 156 " pdb=" O3 NAG T 1 " model vdw 1.282 3.040 nonbonded pdb=" OD1 ASN E 238 " pdb=" C1 NAG E 401 " model vdw 1.375 2.776 nonbonded pdb=" OD1 ASN F 563 " pdb=" C1 NAG S 1 " model vdw 1.376 2.776 nonbonded pdb=" ND2 ASN E 257 " pdb=" C7 NAG R 1 " model vdw 1.412 3.350 nonbonded pdb=" ND2 ASN E 257 " pdb=" N2 NAG R 1 " model vdw 1.478 3.200 ... (remaining 149346 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 33 through 260) selection = (chain 'K' and resid 33 through 260) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'O' } ncs_group { reference = chain 'I' selection = chain 'P' } ncs_group { reference = chain 'J' selection = chain 'Q' } ncs_group { reference = chain 'L' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'R' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.520 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 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 : 0.020 1.452 17348 Z= 1.150 Angle : 2.068 71.033 23590 Z= 1.253 Chirality : 0.194 7.226 2635 Planarity : 0.013 0.161 2987 Dihedral : 11.599 89.571 6050 Min Nonbonded Distance : 1.282 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 1.43 % Allowed : 2.95 % Favored : 95.63 % Rotamer: Outliers : 0.22 % Allowed : 0.22 % Favored : 99.55 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.18), residues: 2105 helix: -1.18 (0.30), residues: 189 sheet: 0.26 (0.19), residues: 622 loop : 1.97 (0.19), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 61 TYR 0.071 0.009 TYR M 534 PHE 0.041 0.006 PHE A 176 TRP 0.071 0.012 TRP F 597 HIS 0.007 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.01380 / 0.86 (17302) covalent geometry : angle 1.81990 / 1.21 (23483) SS BOND : bond 0.03094 / 1.36 ( 25) SS BOND : angle 2.84024 / 2.11 ( 50) hydrogen bonds : bond 0.16598 / 11.30 ( 565) hydrogen bonds : angle 10.65683 / 7.61 ( 1407) Misc. bond : bond 0.27307 / 13.03 ( 2) link_ALPHA1-3 : bond 0.00077 / 0.03 ( 3) link_ALPHA1-3 : angle 0.88664 / 0.44 ( 9) link_ALPHA1-6 : bond 0.00182 / 0.08 ( 3) link_ALPHA1-6 : angle 1.41065 / 0.70 ( 9) link_BETA1-4 : bond 0.00252 / 0.13 ( 9) link_BETA1-4 : angle 1.14035 / 0.71 ( 27) link_NAG-ASN : bond 0.93014 / 46.26 ( 4) link_NAG-ASN : angle 43.40847 / 23.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 352 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 PHE cc_start: 0.8188 (t80) cc_final: 0.7779 (t80) REVERT: B 561 LEU cc_start: 0.9580 (tp) cc_final: 0.9096 (tp) REVERT: B 603 ILE cc_start: 0.5059 (mt) cc_final: 0.3347 (tt) REVERT: C 59 TYR cc_start: 0.9371 (p90) cc_final: 0.9062 (p90) REVERT: C 86 ASP cc_start: 0.8799 (m-30) cc_final: 0.7764 (m-30) REVERT: D 11 LEU cc_start: 0.9124 (tp) cc_final: 0.8764 (tp) REVERT: D 21 ILE cc_start: 0.9307 (mt) cc_final: 0.8982 (tp) REVERT: D 73 LEU cc_start: 0.9361 (tp) cc_final: 0.9073 (tp) REVERT: D 87 PHE cc_start: 0.9371 (m-80) cc_final: 0.9109 (m-10) REVERT: E 120 GLU cc_start: 0.8119 (tt0) cc_final: 0.7867 (tp30) REVERT: E 171 TYR cc_start: 0.9009 (m-80) cc_final: 0.8299 (m-80) REVERT: E 183 PHE cc_start: 0.9219 (m-80) cc_final: 0.8967 (m-80) REVERT: F 603 ILE cc_start: 0.7638 (mt) cc_final: 0.5261 (mt) REVERT: G 82 LEU cc_start: 0.8979 (mt) cc_final: 0.8521 (mt) REVERT: G 90 TYR cc_start: 0.9070 (m-80) cc_final: 0.8792 (m-80) REVERT: H 39 LYS cc_start: 0.9362 (mmmt) cc_final: 0.8904 (mmpt) REVERT: H 61 ARG cc_start: 0.8754 (mtm-85) cc_final: 0.8359 (mtm-85) REVERT: H 73 LEU cc_start: 0.9295 (tp) cc_final: 0.8853 (tp) REVERT: H 78 LEU cc_start: 0.9374 (tp) cc_final: 0.9122 (tp) REVERT: H 86 TYR cc_start: 0.8378 (m-80) cc_final: 0.8015 (m-80) REVERT: H 87 PHE cc_start: 0.8622 (m-80) cc_final: 0.7807 (m-80) REVERT: I 85 ASP cc_start: 0.9325 (m-30) cc_final: 0.8948 (t0) REVERT: J 27 PHE cc_start: 0.7795 (t80) cc_final: 0.7485 (t80) REVERT: J 63 LEU cc_start: 0.8791 (mt) cc_final: 0.8485 (pp) REVERT: N 109 VAL cc_start: 0.9230 (t) cc_final: 0.8681 (t) REVERT: O 21 ILE cc_start: 0.9505 (mt) cc_final: 0.9269 (tp) REVERT: O 30 TYR cc_start: 0.8383 (m-80) cc_final: 0.7896 (m-80) outliers start: 4 outliers final: 2 residues processed: 356 average time/residue: 0.1507 time to fit residues: 77.5437 Evaluate side-chains 190 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 GLN B 551 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS M 551 GLN ** M 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.048855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.040744 restraints weight = 215104.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.041781 restraints weight = 133465.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.042496 restraints weight = 93290.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.043007 restraints weight = 71514.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.043383 restraints weight = 58239.468| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17348 Z= 0.249 Angle : 0.859 12.446 23590 Z= 0.463 Chirality : 0.047 0.247 2635 Planarity : 0.007 0.098 2987 Dihedral : 7.617 79.144 2321 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.90 % Allowed : 3.99 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.18), residues: 2105 helix: -1.12 (0.33), residues: 190 sheet: -0.65 (0.19), residues: 630 loop : 0.85 (0.19), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 596 TYR 0.033 0.003 TYR A 137 PHE 0.031 0.003 PHE Q 98 TRP 0.027 0.003 TRP B 531 HIS 0.008 0.002 HIS O 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.25 (17302) covalent geometry : angle 0.83947 / 0.46 (23483) SS BOND : bond 0.00529 / 0.32 ( 25) SS BOND : angle 1.41432 / 1.00 ( 50) hydrogen bonds : bond 0.05581 / 3.72 ( 565) hydrogen bonds : angle 8.69503 / 6.21 ( 1407) Misc. bond : bond 0.00181 / 0.09 ( 2) link_ALPHA1-3 : bond 0.00394 / 0.20 ( 3) link_ALPHA1-3 : angle 2.00122 / 1.02 ( 9) link_ALPHA1-6 : bond 0.00288 / 0.12 ( 3) link_ALPHA1-6 : angle 1.91694 / 0.98 ( 9) link_BETA1-4 : bond 0.00590 / 0.29 ( 9) link_BETA1-4 : angle 2.53115 / 1.56 ( 27) link_NAG-ASN : bond 0.00774 / 0.39 ( 4) link_NAG-ASN : angle 6.53747 / 4.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 PHE cc_start: 0.8429 (t80) cc_final: 0.7344 (t80) REVERT: B 578 GLU cc_start: 0.8847 (pt0) cc_final: 0.8572 (pt0) REVERT: B 585 LEU cc_start: 0.9105 (pt) cc_final: 0.8902 (pt) REVERT: B 595 GLN cc_start: 0.9460 (mm-40) cc_final: 0.9255 (mm-40) REVERT: C 59 TYR cc_start: 0.9337 (p90) cc_final: 0.9102 (p90) REVERT: C 86 ASP cc_start: 0.8371 (m-30) cc_final: 0.7922 (m-30) REVERT: D 21 ILE cc_start: 0.9344 (mt) cc_final: 0.9090 (tp) REVERT: D 87 PHE cc_start: 0.9266 (m-80) cc_final: 0.8820 (m-80) REVERT: E 120 GLU cc_start: 0.8665 (tt0) cc_final: 0.8302 (tp30) REVERT: E 171 TYR cc_start: 0.9099 (m-80) cc_final: 0.8344 (m-80) REVERT: E 183 PHE cc_start: 0.9492 (m-80) cc_final: 0.9215 (m-80) REVERT: E 301 ILE cc_start: 0.6557 (mm) cc_final: 0.5923 (mm) REVERT: F 595 GLN cc_start: 0.9447 (tm-30) cc_final: 0.9033 (tm-30) REVERT: G 34 MET cc_start: 0.9215 (mmm) cc_final: 0.7639 (tpp) REVERT: H 39 LYS cc_start: 0.9348 (mmmt) cc_final: 0.9127 (pttp) REVERT: I 39 LYS cc_start: 0.9448 (mttt) cc_final: 0.9145 (mmmt) REVERT: I 85 ASP cc_start: 0.9291 (m-30) cc_final: 0.9072 (p0) REVERT: J 53 TRP cc_start: 0.8379 (t-100) cc_final: 0.7800 (t-100) REVERT: M 595 GLN cc_start: 0.9758 (tp40) cc_final: 0.9478 (tm-30) REVERT: N 90 TYR cc_start: 0.8950 (m-10) cc_final: 0.8727 (m-80) REVERT: N 109 VAL cc_start: 0.9363 (t) cc_final: 0.8842 (t) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1595 time to fit residues: 57.9683 Evaluate side-chains 147 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 188 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 165 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 44 GLN K 73 ASN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN P 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.046953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.039001 restraints weight = 222765.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.040002 restraints weight = 136138.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.040708 restraints weight = 94811.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.041206 restraints weight = 72340.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.041563 restraints weight = 59053.393| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17348 Z= 0.223 Angle : 0.773 12.467 23590 Z= 0.415 Chirality : 0.045 0.225 2635 Planarity : 0.006 0.076 2987 Dihedral : 7.285 79.284 2321 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.71 % Allowed : 5.51 % Favored : 93.78 % Rotamer: Outliers : 0.06 % Allowed : 2.12 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.18), residues: 2105 helix: -1.31 (0.32), residues: 187 sheet: -1.03 (0.20), residues: 595 loop : 0.40 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 596 TYR 0.026 0.002 TYR A 137 PHE 0.022 0.002 PHE Q 98 TRP 0.028 0.003 TRP F 531 HIS 0.010 0.002 HIS O 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.22 (17302) covalent geometry : angle 0.75954 / 0.41 (23483) SS BOND : bond 0.00415 / 0.28 ( 25) SS BOND : angle 1.21117 / 0.85 ( 50) hydrogen bonds : bond 0.04924 / 3.24 ( 565) hydrogen bonds : angle 8.17270 / 5.84 ( 1407) Misc. bond : bond 0.00033 / 0.02 ( 2) link_ALPHA1-3 : bond 0.00732 / 0.36 ( 3) link_ALPHA1-3 : angle 1.57507 / 0.85 ( 9) link_ALPHA1-6 : bond 0.00333 / 0.14 ( 3) link_ALPHA1-6 : angle 1.78661 / 0.93 ( 9) link_BETA1-4 : bond 0.00468 / 0.24 ( 9) link_BETA1-4 : angle 1.83580 / 1.12 ( 27) link_NAG-ASN : bond 0.00644 / 0.28 ( 4) link_NAG-ASN : angle 5.27403 / 3.30 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 PHE cc_start: 0.8645 (t80) cc_final: 0.8423 (t80) REVERT: B 578 GLU cc_start: 0.8988 (pt0) cc_final: 0.7568 (mp0) REVERT: C 59 TYR cc_start: 0.9343 (p90) cc_final: 0.9046 (p90) REVERT: C 86 ASP cc_start: 0.8497 (m-30) cc_final: 0.8079 (m-30) REVERT: C 102 TYR cc_start: 0.8548 (p90) cc_final: 0.8339 (p90) REVERT: D 11 LEU cc_start: 0.9258 (tp) cc_final: 0.8928 (tt) REVERT: D 21 ILE cc_start: 0.9463 (mt) cc_final: 0.9218 (tp) REVERT: D 87 PHE cc_start: 0.9273 (m-80) cc_final: 0.9061 (m-10) REVERT: E 51 LEU cc_start: 0.6623 (mt) cc_final: 0.6356 (mt) REVERT: E 120 GLU cc_start: 0.8757 (tt0) cc_final: 0.8359 (tt0) REVERT: E 171 TYR cc_start: 0.9102 (m-80) cc_final: 0.8333 (m-80) REVERT: E 183 PHE cc_start: 0.9418 (m-80) cc_final: 0.9002 (m-80) REVERT: E 301 ILE cc_start: 0.6618 (mm) cc_final: 0.6311 (mm) REVERT: F 595 GLN cc_start: 0.9510 (tm-30) cc_final: 0.9121 (tm-30) REVERT: G 34 MET cc_start: 0.9359 (mmm) cc_final: 0.8966 (mmm) REVERT: H 61 ARG cc_start: 0.9043 (mtm-85) cc_final: 0.8673 (ptt-90) REVERT: H 73 LEU cc_start: 0.9112 (tp) cc_final: 0.8844 (tp) REVERT: H 87 PHE cc_start: 0.8584 (m-80) cc_final: 0.8132 (m-80) REVERT: I 94 TYR cc_start: 0.9255 (p90) cc_final: 0.8916 (p90) REVERT: J 53 TRP cc_start: 0.8429 (t-100) cc_final: 0.7958 (t-100) REVERT: K 51 LEU cc_start: 0.7898 (mp) cc_final: 0.6889 (mp) REVERT: M 595 GLN cc_start: 0.9748 (tp40) cc_final: 0.9304 (tm-30) REVERT: N 109 VAL cc_start: 0.9449 (t) cc_final: 0.8895 (t) REVERT: P 42 GLN cc_start: 0.9613 (mt0) cc_final: 0.9313 (pt0) REVERT: P 73 LEU cc_start: 0.9505 (tt) cc_final: 0.9193 (tt) REVERT: Q 53 TRP cc_start: 0.6816 (m100) cc_final: 0.6480 (m100) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.1576 time to fit residues: 48.3089 Evaluate side-chains 138 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 14 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 27 optimal weight: 0.0070 chunk 112 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 193 optimal weight: 9.9990 overall best weight: 7.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 GLN ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 GLN ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN H 37 GLN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 100BASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.043001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.035219 restraints weight = 232939.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.036159 restraints weight = 144387.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.036814 restraints weight = 101675.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.037285 restraints weight = 78550.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.037615 restraints weight = 64699.073| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 17348 Z= 0.307 Angle : 0.861 11.333 23590 Z= 0.455 Chirality : 0.046 0.262 2635 Planarity : 0.006 0.070 2987 Dihedral : 7.435 82.221 2321 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 30.63 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.51 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.18), residues: 2105 helix: -1.80 (0.29), residues: 213 sheet: -1.34 (0.19), residues: 649 loop : -0.34 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 302 TYR 0.040 0.003 TYR H 86 PHE 0.024 0.003 PHE Q 98 TRP 0.025 0.004 TRP M 597 HIS 0.012 0.002 HIS O 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.31 (17302) covalent geometry : angle 0.84989 / 0.45 (23483) SS BOND : bond 0.00626 / 0.36 ( 25) SS BOND : angle 1.76704 / 1.15 ( 50) hydrogen bonds : bond 0.05326 / 3.54 ( 565) hydrogen bonds : angle 8.40798 / 5.98 ( 1407) Misc. bond : bond 0.00270 / 0.13 ( 2) link_ALPHA1-3 : bond 0.00547 / 0.28 ( 3) link_ALPHA1-3 : angle 1.96018 / 1.05 ( 9) link_ALPHA1-6 : bond 0.00287 / 0.12 ( 3) link_ALPHA1-6 : angle 1.92289 / 0.97 ( 9) link_BETA1-4 : bond 0.00452 / 0.22 ( 9) link_BETA1-4 : angle 2.21600 / 1.31 ( 27) link_NAG-ASN : bond 0.00568 / 0.27 ( 4) link_NAG-ASN : angle 3.84028 / 2.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 PHE cc_start: 0.8977 (t80) cc_final: 0.8607 (t80) REVERT: A 238 ASN cc_start: 0.8631 (t0) cc_final: 0.8429 (p0) REVERT: C 59 TYR cc_start: 0.9432 (p90) cc_final: 0.9043 (p90) REVERT: C 86 ASP cc_start: 0.8492 (m-30) cc_final: 0.8008 (m-30) REVERT: D 11 LEU cc_start: 0.9361 (tp) cc_final: 0.9016 (tt) REVERT: D 87 PHE cc_start: 0.9358 (m-80) cc_final: 0.9025 (m-10) REVERT: E 51 LEU cc_start: 0.6826 (mt) cc_final: 0.6421 (mt) REVERT: E 171 TYR cc_start: 0.9110 (m-80) cc_final: 0.8363 (m-80) REVERT: E 183 PHE cc_start: 0.9214 (m-80) cc_final: 0.8731 (m-10) REVERT: F 595 GLN cc_start: 0.9506 (tm-30) cc_final: 0.9133 (tm-30) REVERT: H 61 ARG cc_start: 0.9023 (mtm-85) cc_final: 0.8715 (ptt180) REVERT: H 73 LEU cc_start: 0.9253 (tp) cc_final: 0.9008 (tp) REVERT: I 94 TYR cc_start: 0.9353 (p90) cc_final: 0.9014 (p90) REVERT: J 53 TRP cc_start: 0.8482 (t-100) cc_final: 0.8009 (t-100) REVERT: M 595 GLN cc_start: 0.9772 (tp40) cc_final: 0.9346 (tm-30) REVERT: N 34 MET cc_start: 0.9119 (tpt) cc_final: 0.8876 (tpp) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1452 time to fit residues: 38.0602 Evaluate side-chains 126 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 168 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 GLN M 567 GLN ** M 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.042836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.035146 restraints weight = 237160.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.036085 restraints weight = 144566.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.036736 restraints weight = 101273.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.037196 restraints weight = 77791.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.037532 restraints weight = 64085.276| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17348 Z= 0.256 Angle : 0.798 11.411 23590 Z= 0.420 Chirality : 0.045 0.251 2635 Planarity : 0.005 0.065 2987 Dihedral : 7.363 87.201 2321 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 27.65 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.03 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.18), residues: 2105 helix: -1.48 (0.32), residues: 204 sheet: -1.54 (0.20), residues: 621 loop : -0.52 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 302 TYR 0.023 0.003 TYR A 137 PHE 0.029 0.003 PHE G 32 TRP 0.018 0.003 TRP K 275 HIS 0.007 0.002 HIS O 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.26 (17302) covalent geometry : angle 0.78896 / 0.42 (23483) SS BOND : bond 0.00539 / 0.33 ( 25) SS BOND : angle 1.23865 / 0.88 ( 50) hydrogen bonds : bond 0.04914 / 3.28 ( 565) hydrogen bonds : angle 8.18261 / 5.86 ( 1407) Misc. bond : bond 0.00074 / 0.04 ( 2) link_ALPHA1-3 : bond 0.00734 / 0.37 ( 3) link_ALPHA1-3 : angle 1.68148 / 0.91 ( 9) link_ALPHA1-6 : bond 0.00313 / 0.12 ( 3) link_ALPHA1-6 : angle 1.78416 / 0.91 ( 9) link_BETA1-4 : bond 0.00432 / 0.21 ( 9) link_BETA1-4 : angle 1.97211 / 1.21 ( 27) link_NAG-ASN : bond 0.00513 / 0.24 ( 4) link_NAG-ASN : angle 3.63978 / 2.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 PHE cc_start: 0.9067 (t80) cc_final: 0.8761 (t80) REVERT: A 238 ASN cc_start: 0.8702 (t0) cc_final: 0.8496 (p0) REVERT: C 59 TYR cc_start: 0.9440 (p90) cc_final: 0.9019 (p90) REVERT: D 87 PHE cc_start: 0.9382 (m-80) cc_final: 0.9052 (m-10) REVERT: E 51 LEU cc_start: 0.6895 (mt) cc_final: 0.6495 (mt) REVERT: E 183 PHE cc_start: 0.9180 (m-80) cc_final: 0.8618 (m-10) REVERT: F 595 GLN cc_start: 0.9450 (tm-30) cc_final: 0.8986 (tm-30) REVERT: H 61 ARG cc_start: 0.9111 (mtm-85) cc_final: 0.8665 (ptt180) REVERT: H 73 LEU cc_start: 0.9207 (tp) cc_final: 0.8956 (tp) REVERT: H 78 LEU cc_start: 0.9686 (tp) cc_final: 0.9470 (tp) REVERT: H 96 PHE cc_start: 0.8665 (m-10) cc_final: 0.8446 (m-10) REVERT: I 94 TYR cc_start: 0.9287 (p90) cc_final: 0.8923 (p90) REVERT: J 53 TRP cc_start: 0.8553 (t-100) cc_final: 0.8092 (t-100) REVERT: K 51 LEU cc_start: 0.8564 (mt) cc_final: 0.7604 (mt) REVERT: M 595 GLN cc_start: 0.9731 (tp40) cc_final: 0.9382 (tm-30) REVERT: N 34 MET cc_start: 0.9179 (tpt) cc_final: 0.8921 (tpp) REVERT: P 28 ASN cc_start: 0.9305 (t0) cc_final: 0.9100 (t0) REVERT: P 73 LEU cc_start: 0.9501 (tt) cc_final: 0.9260 (tt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1439 time to fit residues: 35.4210 Evaluate side-chains 122 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 24 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 191 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 152 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 GLN E 40 ASN E 221 GLN G 39 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.043706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.035883 restraints weight = 233752.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.036840 restraints weight = 141887.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.037498 restraints weight = 98720.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.037970 restraints weight = 75778.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.038297 restraints weight = 62096.146| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17348 Z= 0.192 Angle : 0.732 10.217 23590 Z= 0.384 Chirality : 0.044 0.262 2635 Planarity : 0.005 0.071 2987 Dihedral : 7.119 87.075 2321 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 24.21 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.84 % Favored : 92.40 % Rotamer: Outliers : 0.06 % Allowed : 1.45 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.18), residues: 2105 helix: -1.24 (0.35), residues: 178 sheet: -1.55 (0.19), residues: 631 loop : -0.43 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 302 TYR 0.017 0.002 TYR E 137 PHE 0.026 0.002 PHE O 71 TRP 0.039 0.003 TRP B 531 HIS 0.005 0.001 HIS O 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 (17302) covalent geometry : angle 0.72352 / 0.38 (23483) SS BOND : bond 0.00452 / 0.27 ( 25) SS BOND : angle 1.02651 / 0.73 ( 50) hydrogen bonds : bond 0.04558 / 3.08 ( 565) hydrogen bonds : angle 7.83071 / 5.59 ( 1407) Misc. bond : bond 0.00046 / 0.02 ( 2) link_ALPHA1-3 : bond 0.00720 / 0.36 ( 3) link_ALPHA1-3 : angle 1.52790 / 0.83 ( 9) link_ALPHA1-6 : bond 0.00311 / 0.12 ( 3) link_ALPHA1-6 : angle 1.68671 / 0.86 ( 9) link_BETA1-4 : bond 0.00398 / 0.20 ( 9) link_BETA1-4 : angle 1.85252 / 1.13 ( 27) link_NAG-ASN : bond 0.00332 / 0.15 ( 4) link_NAG-ASN : angle 3.43811 / 1.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 PHE cc_start: 0.9058 (t80) cc_final: 0.8738 (t80) REVERT: C 59 TYR cc_start: 0.9454 (p90) cc_final: 0.9033 (p90) REVERT: D 87 PHE cc_start: 0.9343 (m-80) cc_final: 0.9054 (m-10) REVERT: E 51 LEU cc_start: 0.6878 (mt) cc_final: 0.6467 (mt) REVERT: E 183 PHE cc_start: 0.9185 (m-80) cc_final: 0.8727 (m-10) REVERT: F 595 GLN cc_start: 0.9419 (tm-30) cc_final: 0.8929 (tm-30) REVERT: H 61 ARG cc_start: 0.8998 (mtm-85) cc_final: 0.8769 (ptt180) REVERT: H 73 LEU cc_start: 0.9059 (tp) cc_final: 0.8731 (tp) REVERT: H 78 LEU cc_start: 0.9678 (tp) cc_final: 0.9450 (tp) REVERT: I 94 TYR cc_start: 0.9318 (p90) cc_final: 0.8953 (p90) REVERT: J 53 TRP cc_start: 0.8578 (t-100) cc_final: 0.8132 (t-100) REVERT: M 595 GLN cc_start: 0.9690 (tp40) cc_final: 0.9341 (tm-30) REVERT: N 13 MET cc_start: 0.9051 (ppp) cc_final: 0.8837 (ppp) REVERT: N 34 MET cc_start: 0.9257 (tpt) cc_final: 0.8952 (tpp) REVERT: P 73 LEU cc_start: 0.9508 (tt) cc_final: 0.9241 (tt) REVERT: Q 73 PHE cc_start: 0.8848 (t80) cc_final: 0.8321 (t80) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.1443 time to fit residues: 37.5110 Evaluate side-chains 113 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 5 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 205 optimal weight: 30.0000 chunk 170 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 150 optimal weight: 9.9990 chunk 185 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 GLN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100BASN K 221 GLN M 602 HIS O 37 GLN ** O 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.044644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.036699 restraints weight = 229602.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.037689 restraints weight = 139607.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.038382 restraints weight = 96961.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.038873 restraints weight = 74093.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.039225 restraints weight = 60442.862| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17348 Z= 0.148 Angle : 0.686 12.133 23590 Z= 0.359 Chirality : 0.044 0.264 2635 Planarity : 0.005 0.072 2987 Dihedral : 6.753 80.470 2321 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.89 % Favored : 92.45 % Rotamer: Outliers : 0.06 % Allowed : 1.00 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.18), residues: 2105 helix: -1.25 (0.32), residues: 205 sheet: -1.47 (0.20), residues: 613 loop : -0.55 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 94 TYR 0.015 0.002 TYR J 100 PHE 0.024 0.002 PHE G 32 TRP 0.031 0.002 TRP B 531 HIS 0.004 0.001 HIS B 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (17302) covalent geometry : angle 0.67856 / 0.36 (23483) SS BOND : bond 0.00586 / 0.44 ( 25) SS BOND : angle 1.03226 / 0.71 ( 50) hydrogen bonds : bond 0.04110 / 2.76 ( 565) hydrogen bonds : angle 7.44966 / 5.30 ( 1407) Misc. bond : bond 0.00038 / 0.02 ( 2) link_ALPHA1-3 : bond 0.00779 / 0.38 ( 3) link_ALPHA1-3 : angle 1.42016 / 0.77 ( 9) link_ALPHA1-6 : bond 0.00368 / 0.15 ( 3) link_ALPHA1-6 : angle 1.59412 / 0.82 ( 9) link_BETA1-4 : bond 0.00382 / 0.20 ( 9) link_BETA1-4 : angle 1.67942 / 1.02 ( 27) link_NAG-ASN : bond 0.00268 / 0.13 ( 4) link_NAG-ASN : angle 3.30181 / 1.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9027 (mt) cc_final: 0.8618 (mt) REVERT: A 225 PHE cc_start: 0.9028 (t80) cc_final: 0.8705 (t80) REVERT: C 59 TYR cc_start: 0.9448 (p90) cc_final: 0.9035 (p90) REVERT: D 87 PHE cc_start: 0.9340 (m-80) cc_final: 0.9023 (m-10) REVERT: E 51 LEU cc_start: 0.7000 (mt) cc_final: 0.6522 (mt) REVERT: E 183 PHE cc_start: 0.9221 (m-80) cc_final: 0.8814 (m-10) REVERT: F 595 GLN cc_start: 0.9393 (tm-30) cc_final: 0.8865 (tm-30) REVERT: H 61 ARG cc_start: 0.9013 (mtm-85) cc_final: 0.7860 (ptt180) REVERT: H 73 LEU cc_start: 0.9036 (tp) cc_final: 0.8695 (tp) REVERT: H 78 LEU cc_start: 0.9647 (tp) cc_final: 0.9430 (mt) REVERT: H 79 GLN cc_start: 0.9511 (mm-40) cc_final: 0.9022 (mp10) REVERT: I 94 TYR cc_start: 0.9304 (p90) cc_final: 0.8909 (p90) REVERT: J 27 PHE cc_start: 0.8259 (t80) cc_final: 0.8037 (t80) REVERT: J 53 TRP cc_start: 0.8584 (t-100) cc_final: 0.8144 (t-100) REVERT: J 100 MET cc_start: 0.9127 (tpp) cc_final: 0.8535 (mmm) REVERT: J 102 TYR cc_start: 0.9012 (t80) cc_final: 0.8326 (t80) REVERT: M 595 GLN cc_start: 0.9688 (tp40) cc_final: 0.9355 (tm-30) REVERT: N 13 MET cc_start: 0.9071 (ppp) cc_final: 0.8865 (ppp) REVERT: N 34 MET cc_start: 0.9266 (tpt) cc_final: 0.8961 (tpp) REVERT: P 28 ASN cc_start: 0.9306 (t0) cc_final: 0.9043 (t0) REVERT: P 73 LEU cc_start: 0.9538 (tt) cc_final: 0.9278 (tt) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.1385 time to fit residues: 36.1755 Evaluate side-chains 121 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 182 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 161 optimal weight: 0.6980 chunk 109 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 162 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 278 ASN M 602 HIS ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.043743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.035804 restraints weight = 235518.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.036774 restraints weight = 142564.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.037456 restraints weight = 99173.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.037950 restraints weight = 75722.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.038292 restraints weight = 61835.859| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17348 Z= 0.173 Angle : 0.699 10.055 23590 Z= 0.367 Chirality : 0.044 0.268 2635 Planarity : 0.005 0.088 2987 Dihedral : 6.635 75.186 2321 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 23.34 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.17 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.18), residues: 2105 helix: -1.21 (0.33), residues: 194 sheet: -1.51 (0.19), residues: 619 loop : -0.65 (0.18), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 302 TYR 0.024 0.002 TYR C 98 PHE 0.024 0.002 PHE G 32 TRP 0.031 0.003 TRP B 531 HIS 0.004 0.001 HIS O 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (17302) covalent geometry : angle 0.69131 / 0.37 (23483) SS BOND : bond 0.00418 / 0.26 ( 25) SS BOND : angle 1.17414 / 0.81 ( 50) hydrogen bonds : bond 0.04176 / 2.78 ( 565) hydrogen bonds : angle 7.41081 / 5.29 ( 1407) Misc. bond : bond 0.00055 / 0.03 ( 2) link_ALPHA1-3 : bond 0.00757 / 0.37 ( 3) link_ALPHA1-3 : angle 1.53829 / 0.84 ( 9) link_ALPHA1-6 : bond 0.00301 / 0.12 ( 3) link_ALPHA1-6 : angle 1.63109 / 0.84 ( 9) link_BETA1-4 : bond 0.00321 / 0.17 ( 9) link_BETA1-4 : angle 1.71075 / 1.03 ( 27) link_NAG-ASN : bond 0.00261 / 0.12 ( 4) link_NAG-ASN : angle 3.17422 / 1.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8824 (mt) cc_final: 0.8585 (mt) REVERT: A 225 PHE cc_start: 0.9077 (t80) cc_final: 0.8734 (t80) REVERT: B 603 ILE cc_start: 0.9117 (tt) cc_final: 0.8866 (tt) REVERT: C 59 TYR cc_start: 0.9446 (p90) cc_final: 0.9048 (p90) REVERT: D 87 PHE cc_start: 0.9329 (m-80) cc_final: 0.9076 (m-10) REVERT: E 51 LEU cc_start: 0.7016 (mt) cc_final: 0.6550 (mt) REVERT: E 183 PHE cc_start: 0.9198 (m-80) cc_final: 0.8798 (m-10) REVERT: F 595 GLN cc_start: 0.9376 (tm-30) cc_final: 0.8860 (tm-30) REVERT: H 61 ARG cc_start: 0.9034 (mtm-85) cc_final: 0.7874 (ptt180) REVERT: H 73 LEU cc_start: 0.9042 (tp) cc_final: 0.8693 (tp) REVERT: H 78 LEU cc_start: 0.9631 (tp) cc_final: 0.9413 (mt) REVERT: H 79 GLN cc_start: 0.9536 (mm-40) cc_final: 0.9062 (mp10) REVERT: I 94 TYR cc_start: 0.9314 (p90) cc_final: 0.8945 (p90) REVERT: J 27 PHE cc_start: 0.8272 (t80) cc_final: 0.8034 (t80) REVERT: J 53 TRP cc_start: 0.8590 (t-100) cc_final: 0.8126 (t-100) REVERT: J 100 MET cc_start: 0.9181 (tpp) cc_final: 0.8532 (mmm) REVERT: J 102 TYR cc_start: 0.9066 (t80) cc_final: 0.8364 (t80) REVERT: M 595 GLN cc_start: 0.9693 (tp40) cc_final: 0.9361 (tm-30) REVERT: N 34 MET cc_start: 0.9289 (tpt) cc_final: 0.8981 (tpp) REVERT: P 4 MET cc_start: 0.7759 (pmm) cc_final: 0.7236 (pmm) REVERT: P 28 ASN cc_start: 0.9332 (t0) cc_final: 0.9097 (t0) REVERT: P 73 LEU cc_start: 0.9560 (tt) cc_final: 0.9279 (tt) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1428 time to fit residues: 35.1717 Evaluate side-chains 120 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 182 optimal weight: 10.0000 chunk 199 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 189 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 196 optimal weight: 20.0000 chunk 152 optimal weight: 7.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 ASN I 37 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.042131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.034374 restraints weight = 237786.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.035278 restraints weight = 144654.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.035914 restraints weight = 101346.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.036374 restraints weight = 78267.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.036700 restraints weight = 64625.004| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 17348 Z= 0.233 Angle : 0.763 9.537 23590 Z= 0.401 Chirality : 0.045 0.263 2635 Planarity : 0.005 0.091 2987 Dihedral : 6.794 78.276 2321 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 27.77 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.65 % Favored : 90.69 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.18), residues: 2105 helix: -1.43 (0.32), residues: 203 sheet: -1.70 (0.19), residues: 649 loop : -0.80 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 302 TYR 0.026 0.002 TYR N 91 PHE 0.033 0.003 PHE K 132 TRP 0.030 0.003 TRP F 531 HIS 0.005 0.001 HIS O 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.23 (17302) covalent geometry : angle 0.75460 / 0.40 (23483) SS BOND : bond 0.00474 / 0.27 ( 25) SS BOND : angle 1.33060 / 0.91 ( 50) hydrogen bonds : bond 0.04627 / 3.11 ( 565) hydrogen bonds : angle 7.68252 / 5.47 ( 1407) Misc. bond : bond 0.00083 / 0.04 ( 2) link_ALPHA1-3 : bond 0.00714 / 0.35 ( 3) link_ALPHA1-3 : angle 1.58403 / 0.87 ( 9) link_ALPHA1-6 : bond 0.00235 / 0.09 ( 3) link_ALPHA1-6 : angle 1.73916 / 0.87 ( 9) link_BETA1-4 : bond 0.00387 / 0.20 ( 9) link_BETA1-4 : angle 1.88458 / 1.13 ( 27) link_NAG-ASN : bond 0.00409 / 0.18 ( 4) link_NAG-ASN : angle 3.10239 / 1.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8783 (mt) cc_final: 0.8554 (mt) REVERT: A 225 PHE cc_start: 0.9126 (t80) cc_final: 0.8776 (t80) REVERT: B 578 GLU cc_start: 0.9152 (pt0) cc_final: 0.8123 (mp0) REVERT: C 59 TYR cc_start: 0.9453 (p90) cc_final: 0.9135 (p90) REVERT: E 51 LEU cc_start: 0.6807 (mt) cc_final: 0.6585 (mt) REVERT: E 183 PHE cc_start: 0.9239 (m-80) cc_final: 0.8829 (m-10) REVERT: F 595 GLN cc_start: 0.9361 (tm-30) cc_final: 0.8977 (tm-30) REVERT: H 78 LEU cc_start: 0.9658 (tp) cc_final: 0.9396 (tp) REVERT: H 79 GLN cc_start: 0.9545 (mm-40) cc_final: 0.9110 (mm-40) REVERT: I 94 TYR cc_start: 0.9329 (p90) cc_final: 0.9007 (p90) REVERT: J 53 TRP cc_start: 0.8616 (t-100) cc_final: 0.8177 (t-100) REVERT: J 102 TYR cc_start: 0.9081 (t80) cc_final: 0.8425 (t80) REVERT: M 595 GLN cc_start: 0.9717 (tp40) cc_final: 0.9383 (tm-30) REVERT: N 34 MET cc_start: 0.9276 (tpt) cc_final: 0.8989 (tpp) REVERT: N 79 TYR cc_start: 0.9575 (m-10) cc_final: 0.9178 (m-80) REVERT: P 4 MET cc_start: 0.7883 (pmm) cc_final: 0.7293 (pmm) REVERT: P 28 ASN cc_start: 0.9268 (t0) cc_final: 0.9039 (t0) REVERT: P 73 LEU cc_start: 0.9583 (tt) cc_final: 0.9300 (tt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1348 time to fit residues: 32.9314 Evaluate side-chains 116 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 144 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** 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 = 0.3426 r_free = 0.3426 target = 0.041738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.033985 restraints weight = 238417.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.034890 restraints weight = 145525.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.035519 restraints weight = 102617.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.035970 restraints weight = 79337.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.036271 restraints weight = 65385.601| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.6215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 17348 Z= 0.239 Angle : 0.776 10.415 23590 Z= 0.407 Chirality : 0.046 0.264 2635 Planarity : 0.005 0.088 2987 Dihedral : 6.840 80.348 2321 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 29.54 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.98 % Favored : 90.36 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.18), residues: 2105 helix: -1.45 (0.32), residues: 205 sheet: -1.76 (0.18), residues: 683 loop : -0.92 (0.19), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 302 TYR 0.028 0.003 TYR G 90 PHE 0.044 0.003 PHE K 132 TRP 0.027 0.003 TRP F 531 HIS 0.006 0.002 HIS O 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.24 (17302) covalent geometry : angle 0.76742 / 0.41 (23483) SS BOND : bond 0.00534 / 0.32 ( 25) SS BOND : angle 1.46624 / 1.11 ( 50) hydrogen bonds : bond 0.04678 / 3.15 ( 565) hydrogen bonds : angle 7.76925 / 5.53 ( 1407) Misc. bond : bond 0.00070 / 0.03 ( 2) link_ALPHA1-3 : bond 0.00709 / 0.35 ( 3) link_ALPHA1-3 : angle 1.52849 / 0.84 ( 9) link_ALPHA1-6 : bond 0.00280 / 0.11 ( 3) link_ALPHA1-6 : angle 1.78073 / 0.90 ( 9) link_BETA1-4 : bond 0.00361 / 0.18 ( 9) link_BETA1-4 : angle 1.98288 / 1.21 ( 27) link_NAG-ASN : bond 0.00555 / 0.23 ( 4) link_NAG-ASN : angle 3.22508 / 1.84 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8770 (mt) cc_final: 0.8533 (mt) REVERT: A 225 PHE cc_start: 0.9140 (t80) cc_final: 0.8792 (t80) REVERT: B 578 GLU cc_start: 0.9180 (pt0) cc_final: 0.8175 (mp0) REVERT: C 59 TYR cc_start: 0.9417 (p90) cc_final: 0.9071 (p90) REVERT: E 183 PHE cc_start: 0.9204 (m-80) cc_final: 0.8820 (m-10) REVERT: F 595 GLN cc_start: 0.9351 (tm-30) cc_final: 0.8907 (tm-30) REVERT: H 73 LEU cc_start: 0.9258 (tp) cc_final: 0.9017 (tp) REVERT: H 78 LEU cc_start: 0.9663 (tp) cc_final: 0.9406 (tp) REVERT: H 79 GLN cc_start: 0.9506 (mm-40) cc_final: 0.9078 (mm-40) REVERT: I 94 TYR cc_start: 0.9327 (p90) cc_final: 0.9050 (p90) REVERT: J 27 PHE cc_start: 0.8540 (t80) cc_final: 0.8238 (t80) REVERT: J 53 TRP cc_start: 0.8671 (t-100) cc_final: 0.8258 (t-100) REVERT: J 102 TYR cc_start: 0.8915 (t80) cc_final: 0.8319 (t80) REVERT: M 595 GLN cc_start: 0.9725 (tp40) cc_final: 0.9392 (tm-30) REVERT: N 34 MET cc_start: 0.9275 (tpt) cc_final: 0.8989 (tpp) REVERT: N 79 TYR cc_start: 0.9584 (m-10) cc_final: 0.9123 (m-80) REVERT: P 4 MET cc_start: 0.7875 (pmm) cc_final: 0.7293 (pmm) REVERT: P 28 ASN cc_start: 0.9300 (t0) cc_final: 0.9084 (t0) REVERT: P 73 LEU cc_start: 0.9587 (tt) cc_final: 0.9317 (tt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1503 time to fit residues: 35.4151 Evaluate side-chains 114 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 46 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 186 optimal weight: 8.9990 chunk 18 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.042051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.034342 restraints weight = 236502.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.035265 restraints weight = 143874.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.035887 restraints weight = 100769.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.036336 restraints weight = 78046.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.036667 restraints weight = 64469.710| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.6331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17348 Z= 0.200 Angle : 0.741 9.425 23590 Z= 0.388 Chirality : 0.045 0.268 2635 Planarity : 0.005 0.086 2987 Dihedral : 6.725 80.747 2321 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 27.62 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.50 % Favored : 90.83 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.18), residues: 2105 helix: -1.27 (0.33), residues: 205 sheet: -1.76 (0.18), residues: 684 loop : -0.94 (0.19), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 302 TYR 0.019 0.002 TYR N 90 PHE 0.027 0.002 PHE K 132 TRP 0.024 0.003 TRP B 531 HIS 0.005 0.001 HIS O 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 (17302) covalent geometry : angle 0.73276 / 0.39 (23483) SS BOND : bond 0.00522 / 0.33 ( 25) SS BOND : angle 1.28972 / 0.93 ( 50) hydrogen bonds : bond 0.04462 / 3.02 ( 565) hydrogen bonds : angle 7.62987 / 5.43 ( 1407) Misc. bond : bond 0.00057 / 0.03 ( 2) link_ALPHA1-3 : bond 0.00731 / 0.36 ( 3) link_ALPHA1-3 : angle 1.42172 / 0.78 ( 9) link_ALPHA1-6 : bond 0.00345 / 0.14 ( 3) link_ALPHA1-6 : angle 1.76131 / 0.89 ( 9) link_BETA1-4 : bond 0.00352 / 0.18 ( 9) link_BETA1-4 : angle 1.90933 / 1.17 ( 27) link_NAG-ASN : bond 0.00316 / 0.15 ( 4) link_NAG-ASN : angle 3.13011 / 1.82 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2905.02 seconds wall clock time: 51 minutes 38.69 seconds (3098.69 seconds total)