Starting phenix.real_space_refine on Thu Sep 18 13:29:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ken_8242/09_2025/5ken_8242.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ken_8242/09_2025/5ken_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5ken_8242/09_2025/5ken_8242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ken_8242/09_2025/5ken_8242.map" model { file = "/net/cci-nas-00/data/ceres_data/5ken_8242/09_2025/5ken_8242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ken_8242/09_2025/5ken_8242.cif" } 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-2.0-5805/lib/python3.9/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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.84, 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: 1.50 Conformation dependent library (CDL) restraints added in 757.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.67 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: 2.69 Time building geometry restraints manager: 1.98 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 - 21.20: 10057 21.20 - 42.39: 270 42.39 - 63.59: 97 63.59 - 84.78: 52 84.78 - 105.98: 19 Dihedral angle restraints: 10495 sinusoidal: 4384 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 10492 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.120 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 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 : 13.218 105.976 6536 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 aren 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 covalent geometry : bond 0.01380 (17302) covalent geometry : angle 1.81990 (23483) SS BOND : bond 0.03094 ( 25) SS BOND : angle 2.84024 ( 50) hydrogen bonds : bond 0.16598 ( 565) hydrogen bonds : angle 10.65683 ( 1407) Misc. bond : bond 0.27307 ( 2) link_ALPHA1-3 : bond 0.00077 ( 3) link_ALPHA1-3 : angle 0.88664 ( 9) link_ALPHA1-6 : bond 0.00182 ( 3) link_ALPHA1-6 : angle 1.41065 ( 9) link_BETA1-4 : bond 0.00252 ( 9) link_BETA1-4 : angle 1.14035 ( 27) link_NAG-ASN : bond 0.93014 ( 4) link_NAG-ASN : angle 43.40847 ( 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 : 0.657 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: 0.1412 time to fit residues: 71.9794 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 : 0.695 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 GLN B 551 GLN D 89 GLN ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 HIS ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS K 268 ASN M 551 GLN M 602 HIS N 61 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.048759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.040657 restraints weight = 214925.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.041704 restraints weight = 132410.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.042399 restraints weight = 92521.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.042899 restraints weight = 70997.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.043284 restraints weight = 58050.562| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17348 Z= 0.248 Angle : 0.861 13.105 23590 Z= 0.462 Chirality : 0.048 0.280 2635 Planarity : 0.007 0.100 2987 Dihedral : 11.388 82.905 2807 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.90 % Allowed : 4.13 % Favored : 94.96 % Rotamer: Outliers : 0.06 % Allowed : 1.56 % Favored : 98.38 % 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 aren not related in a simple way. whole: 0.04 (0.18), residues: 2105 helix: -1.19 (0.33), residues: 190 sheet: -0.66 (0.19), residues: 630 loop : 0.80 (0.18), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 247 TYR 0.034 0.003 TYR A 137 PHE 0.032 0.003 PHE Q 98 TRP 0.028 0.003 TRP F 531 HIS 0.009 0.002 HIS O 91 Details of bonding type rmsd covalent geometry : bond 0.00515 (17302) covalent geometry : angle 0.84021 (23483) SS BOND : bond 0.00509 ( 25) SS BOND : angle 1.37976 ( 50) hydrogen bonds : bond 0.05550 ( 565) hydrogen bonds : angle 8.66813 ( 1407) Misc. bond : bond 0.00387 ( 2) link_ALPHA1-3 : bond 0.01022 ( 3) link_ALPHA1-3 : angle 3.14448 ( 9) link_ALPHA1-6 : bond 0.00507 ( 3) link_ALPHA1-6 : angle 2.55368 ( 9) link_BETA1-4 : bond 0.00634 ( 9) link_BETA1-4 : angle 2.52590 ( 27) link_NAG-ASN : bond 0.01058 ( 4) link_NAG-ASN : angle 6.48164 ( 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 251 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 0.616 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: A 132 PHE cc_start: 0.8430 (t80) cc_final: 0.7340 (t80) REVERT: B 578 GLU cc_start: 0.8895 (pt0) cc_final: 0.8634 (pt0) REVERT: B 585 LEU cc_start: 0.9114 (pt) cc_final: 0.8910 (pt) REVERT: B 595 GLN cc_start: 0.9463 (mm-40) cc_final: 0.9242 (mm-40) REVERT: C 59 TYR cc_start: 0.9343 (p90) cc_final: 0.9108 (p90) REVERT: C 86 ASP cc_start: 0.8395 (m-30) cc_final: 0.7935 (m-30) REVERT: D 21 ILE cc_start: 0.9349 (mt) cc_final: 0.9092 (tp) REVERT: D 87 PHE cc_start: 0.9302 (m-80) cc_final: 0.8841 (m-80) REVERT: E 120 GLU cc_start: 0.8673 (tt0) cc_final: 0.8308 (tp30) REVERT: E 171 TYR cc_start: 0.9102 (m-80) cc_final: 0.8350 (m-80) REVERT: E 183 PHE cc_start: 0.9478 (m-80) cc_final: 0.9168 (m-80) REVERT: E 301 ILE cc_start: 0.6563 (mm) cc_final: 0.5928 (mm) REVERT: F 595 GLN cc_start: 0.9456 (tm-30) cc_final: 0.9042 (tm-30) REVERT: G 34 MET cc_start: 0.9192 (mmm) cc_final: 0.7447 (tpp) REVERT: G 90 TYR cc_start: 0.8771 (m-80) cc_final: 0.8557 (m-80) REVERT: H 39 LYS cc_start: 0.9346 (mmmt) cc_final: 0.9059 (pttp) REVERT: H 61 ARG cc_start: 0.8875 (mtm-85) cc_final: 0.8648 (ptt-90) REVERT: H 62 PHE cc_start: 0.7946 (m-10) cc_final: 0.7509 (m-10) REVERT: I 85 ASP cc_start: 0.9296 (m-30) cc_final: 0.8948 (p0) REVERT: J 53 TRP cc_start: 0.8394 (t-100) cc_final: 0.7824 (t-100) REVERT: J 72 ASP cc_start: 0.9308 (t0) cc_final: 0.8960 (t70) REVERT: M 595 GLN cc_start: 0.9763 (tp40) cc_final: 0.9489 (tm-30) REVERT: N 90 TYR cc_start: 0.8948 (m-10) cc_final: 0.8737 (m-80) REVERT: N 109 VAL cc_start: 0.9370 (t) cc_final: 0.8866 (t) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.1404 time to fit residues: 50.9019 Evaluate side-chains 149 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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: 7.9990 chunk 157 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 20.0000 chunk 165 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN E 221 GLN ** 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** J 77 GLN J 100BASN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.048928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.040781 restraints weight = 217782.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.041869 restraints weight = 132975.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.042613 restraints weight = 91876.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.043143 restraints weight = 69509.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.043520 restraints weight = 56275.068| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17348 Z= 0.167 Angle : 0.733 11.343 23590 Z= 0.390 Chirality : 0.046 0.251 2635 Planarity : 0.005 0.077 2987 Dihedral : 10.260 78.849 2807 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.76 % Allowed : 4.89 % Favored : 94.35 % Rotamer: Outliers : 0.17 % Allowed : 1.78 % Favored : 98.05 % 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 aren not related in a simple way. whole: -0.32 (0.18), residues: 2105 helix: -1.04 (0.34), residues: 185 sheet: -1.01 (0.19), residues: 610 loop : 0.50 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 247 TYR 0.023 0.002 TYR A 137 PHE 0.020 0.002 PHE O 71 TRP 0.023 0.003 TRP M 531 HIS 0.006 0.001 HIS O 91 Details of bonding type rmsd covalent geometry : bond 0.00358 (17302) covalent geometry : angle 0.71690 (23483) SS BOND : bond 0.00612 ( 25) SS BOND : angle 1.10636 ( 50) hydrogen bonds : bond 0.04596 ( 565) hydrogen bonds : angle 7.95190 ( 1407) Misc. bond : bond 0.00031 ( 2) link_ALPHA1-3 : bond 0.01209 ( 3) link_ALPHA1-3 : angle 2.11107 ( 9) link_ALPHA1-6 : bond 0.00702 ( 3) link_ALPHA1-6 : angle 2.27418 ( 9) link_BETA1-4 : bond 0.00483 ( 9) link_BETA1-4 : angle 1.80637 ( 27) link_NAG-ASN : bond 0.00470 ( 4) link_NAG-ASN : angle 5.43717 ( 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 221 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 218 time to evaluate : 0.552 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 225 PHE cc_start: 0.8544 (t80) cc_final: 0.8334 (t80) REVERT: B 578 GLU cc_start: 0.9031 (pt0) cc_final: 0.8821 (pt0) REVERT: C 59 TYR cc_start: 0.9310 (p90) cc_final: 0.9087 (p90) REVERT: C 86 ASP cc_start: 0.8510 (m-30) cc_final: 0.7955 (m-30) REVERT: D 21 ILE cc_start: 0.9400 (mt) cc_final: 0.9155 (tp) REVERT: E 171 TYR cc_start: 0.9062 (m-80) cc_final: 0.8209 (m-80) REVERT: E 183 PHE cc_start: 0.9383 (m-80) cc_final: 0.9004 (m-80) REVERT: E 301 ILE cc_start: 0.6472 (mm) cc_final: 0.6160 (mm) REVERT: F 595 GLN cc_start: 0.9462 (tm-30) cc_final: 0.9190 (tm-30) REVERT: G 34 MET cc_start: 0.9353 (mmm) cc_final: 0.8869 (mmm) REVERT: H 61 ARG cc_start: 0.9042 (mtm-85) cc_final: 0.8812 (ptt180) REVERT: H 73 LEU cc_start: 0.9093 (tp) cc_final: 0.8683 (tp) REVERT: I 85 ASP cc_start: 0.9363 (m-30) cc_final: 0.8981 (p0) REVERT: I 94 TYR cc_start: 0.9273 (p90) cc_final: 0.8877 (p90) REVERT: J 53 TRP cc_start: 0.8383 (t-100) cc_final: 0.7896 (t-100) REVERT: J 72 ASP cc_start: 0.9418 (t0) cc_final: 0.9017 (t70) REVERT: J 75 ARG cc_start: 0.9645 (ttp-110) cc_final: 0.9444 (ttp-110) REVERT: K 51 LEU cc_start: 0.7762 (mp) cc_final: 0.7349 (mt) REVERT: M 595 GLN cc_start: 0.9735 (tp40) cc_final: 0.9482 (tp40) REVERT: N 109 VAL cc_start: 0.9383 (t) cc_final: 0.8783 (t) REVERT: Q 53 TRP cc_start: 0.6770 (m100) cc_final: 0.6420 (m100) outliers start: 3 outliers final: 0 residues processed: 221 average time/residue: 0.1355 time to fit residues: 43.5453 Evaluate side-chains 150 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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: 20.0000 chunk 92 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 193 optimal weight: 4.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 HIS ** 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.046795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.038812 restraints weight = 220736.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.039821 restraints weight = 134405.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.040515 restraints weight = 93293.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.041018 restraints weight = 71316.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.041340 restraints weight = 58039.451| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17348 Z= 0.190 Angle : 0.724 10.821 23590 Z= 0.382 Chirality : 0.044 0.241 2635 Planarity : 0.005 0.067 2987 Dihedral : 9.603 79.909 2807 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.76 % Allowed : 5.27 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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 aren not related in a simple way. whole: -0.55 (0.18), residues: 2105 helix: -0.96 (0.35), residues: 184 sheet: -1.09 (0.20), residues: 600 loop : 0.24 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 302 TYR 0.022 0.002 TYR G 90 PHE 0.021 0.002 PHE O 71 TRP 0.022 0.003 TRP B 531 HIS 0.007 0.001 HIS O 91 Details of bonding type rmsd covalent geometry : bond 0.00398 (17302) covalent geometry : angle 0.70961 (23483) SS BOND : bond 0.00400 ( 25) SS BOND : angle 1.24603 ( 50) hydrogen bonds : bond 0.04451 ( 565) hydrogen bonds : angle 7.76727 ( 1407) Misc. bond : bond 0.00051 ( 2) link_ALPHA1-3 : bond 0.01469 ( 3) link_ALPHA1-3 : angle 2.69741 ( 9) link_ALPHA1-6 : bond 0.00667 ( 3) link_ALPHA1-6 : angle 2.22735 ( 9) link_BETA1-4 : bond 0.00485 ( 9) link_BETA1-4 : angle 1.69253 ( 27) link_NAG-ASN : bond 0.00154 ( 4) link_NAG-ASN : angle 4.69765 ( 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 199 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.477 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: A 225 PHE cc_start: 0.8744 (t80) cc_final: 0.8486 (t80) REVERT: A 238 ASN cc_start: 0.8714 (t0) cc_final: 0.8480 (p0) REVERT: B 578 GLU cc_start: 0.9038 (pt0) cc_final: 0.7681 (mp0) REVERT: B 583 SER cc_start: 0.9185 (p) cc_final: 0.8922 (m) REVERT: C 59 TYR cc_start: 0.9384 (p90) cc_final: 0.9052 (p90) REVERT: C 80 MET cc_start: 0.9354 (ttp) cc_final: 0.8759 (tmm) REVERT: C 82 LEU cc_start: 0.9305 (mp) cc_final: 0.8881 (mp) REVERT: C 86 ASP cc_start: 0.8541 (m-30) cc_final: 0.8037 (m-30) REVERT: C 102 TYR cc_start: 0.8514 (p90) cc_final: 0.8281 (p90) REVERT: D 11 LEU cc_start: 0.9333 (tp) cc_final: 0.8993 (tt) REVERT: E 51 LEU cc_start: 0.6629 (mt) cc_final: 0.6279 (mt) REVERT: E 171 TYR cc_start: 0.9131 (m-80) cc_final: 0.8330 (m-80) REVERT: E 301 ILE cc_start: 0.6491 (mm) cc_final: 0.6155 (mm) REVERT: F 595 GLN cc_start: 0.9453 (tm-30) cc_final: 0.8982 (tm-30) REVERT: G 34 MET cc_start: 0.9381 (mmm) cc_final: 0.8785 (mmm) REVERT: H 61 ARG cc_start: 0.9040 (mtm-85) cc_final: 0.8776 (ptt-90) REVERT: H 73 LEU cc_start: 0.9057 (tp) cc_final: 0.8829 (tp) REVERT: H 96 PHE cc_start: 0.8812 (m-10) cc_final: 0.8490 (m-10) REVERT: I 85 ASP cc_start: 0.9380 (m-30) cc_final: 0.8950 (p0) REVERT: I 94 TYR cc_start: 0.9267 (p90) cc_final: 0.8939 (p90) REVERT: J 53 TRP cc_start: 0.8358 (t-100) cc_final: 0.7883 (t-100) REVERT: J 100 MET cc_start: 0.8706 (mmp) cc_final: 0.7967 (tpp) REVERT: M 595 GLN cc_start: 0.9704 (tp40) cc_final: 0.9348 (tm-30) REVERT: M 602 HIS cc_start: 0.8941 (t-170) cc_final: 0.8703 (t-170) REVERT: N 34 MET cc_start: 0.9104 (tpt) cc_final: 0.8895 (tpp) REVERT: N 109 VAL cc_start: 0.9440 (t) cc_final: 0.8943 (t) REVERT: P 28 ASN cc_start: 0.9241 (t0) cc_final: 0.9040 (t0) REVERT: P 42 GLN cc_start: 0.9568 (mt0) cc_final: 0.9247 (pt0) REVERT: Q 53 TRP cc_start: 0.6840 (m100) cc_final: 0.6479 (m100) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1307 time to fit residues: 37.9355 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 : 0.517 ------------------------------------------------------------------------------- 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: 9.9990 chunk 15 optimal weight: 0.0670 chunk 14 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 63 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 overall best weight: 4.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 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 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** H 76 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** J 66 GLN M 567 GLN ** 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** Q 100BASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.045184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.037316 restraints weight = 223905.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.038264 restraints weight = 136850.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.038947 restraints weight = 96181.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.039436 restraints weight = 73886.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.039772 restraints weight = 60616.570| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17348 Z= 0.209 Angle : 0.732 9.365 23590 Z= 0.386 Chirality : 0.044 0.244 2635 Planarity : 0.005 0.070 2987 Dihedral : 9.182 82.315 2807 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.76 % Allowed : 5.70 % Favored : 93.54 % 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 : 0.10 % 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 aren not related in a simple way. whole: -0.78 (0.19), residues: 2105 helix: -0.90 (0.36), residues: 172 sheet: -1.27 (0.20), residues: 604 loop : 0.04 (0.18), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 302 TYR 0.021 0.002 TYR C 98 PHE 0.029 0.002 PHE H 87 TRP 0.018 0.003 TRP B 531 HIS 0.008 0.002 HIS O 91 Details of bonding type rmsd covalent geometry : bond 0.00437 (17302) covalent geometry : angle 0.71849 (23483) SS BOND : bond 0.00465 ( 25) SS BOND : angle 1.14343 ( 50) hydrogen bonds : bond 0.04462 ( 565) hydrogen bonds : angle 7.69507 ( 1407) Misc. bond : bond 0.00098 ( 2) link_ALPHA1-3 : bond 0.01185 ( 3) link_ALPHA1-3 : angle 2.44849 ( 9) link_ALPHA1-6 : bond 0.00630 ( 3) link_ALPHA1-6 : angle 2.04106 ( 9) link_BETA1-4 : bond 0.00448 ( 9) link_BETA1-4 : angle 1.75836 ( 27) link_NAG-ASN : bond 0.00290 ( 4) link_NAG-ASN : angle 4.82156 ( 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 183 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.705 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: 0.8901 (t80) cc_final: 0.8563 (t80) REVERT: C 59 TYR cc_start: 0.9379 (p90) cc_final: 0.9026 (p90) REVERT: C 86 ASP cc_start: 0.8552 (m-30) cc_final: 0.8121 (m-30) REVERT: C 102 TYR cc_start: 0.8536 (p90) cc_final: 0.8320 (p90) REVERT: D 11 LEU cc_start: 0.9357 (tp) cc_final: 0.9032 (tt) REVERT: D 87 PHE cc_start: 0.9349 (m-80) cc_final: 0.9135 (m-10) REVERT: E 51 LEU cc_start: 0.6779 (mt) cc_final: 0.6427 (mt) REVERT: E 171 TYR cc_start: 0.9149 (m-80) cc_final: 0.8454 (m-80) REVERT: F 595 GLN cc_start: 0.9453 (tm-30) cc_final: 0.9002 (tm-30) REVERT: G 34 MET cc_start: 0.8950 (mmm) cc_final: 0.8649 (mmm) REVERT: G 36 TRP cc_start: 0.9368 (m100) cc_final: 0.9108 (m100) REVERT: H 61 ARG cc_start: 0.9048 (mtm-85) cc_final: 0.8503 (ptt180) REVERT: H 73 LEU cc_start: 0.9165 (tp) cc_final: 0.8834 (tp) REVERT: H 78 LEU cc_start: 0.9711 (tp) cc_final: 0.9380 (tp) REVERT: H 79 GLN cc_start: 0.9561 (mm-40) cc_final: 0.9137 (mp10) REVERT: H 87 PHE cc_start: 0.8472 (m-80) cc_final: 0.8111 (m-80) REVERT: H 96 PHE cc_start: 0.8778 (m-10) cc_final: 0.8561 (m-10) REVERT: I 94 TYR cc_start: 0.9321 (p90) cc_final: 0.8987 (p90) REVERT: J 53 TRP cc_start: 0.8406 (t-100) cc_final: 0.7922 (t-100) REVERT: J 102 TYR cc_start: 0.8975 (t80) cc_final: 0.8389 (t80) REVERT: N 34 MET cc_start: 0.9162 (tpt) cc_final: 0.8940 (tpp) REVERT: N 79 TYR cc_start: 0.9482 (m-10) cc_final: 0.9111 (m-80) REVERT: N 109 VAL cc_start: 0.9469 (t) cc_final: 0.9000 (t) REVERT: P 73 LEU cc_start: 0.9467 (tt) cc_final: 0.9173 (tt) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1373 time to fit residues: 37.3067 Evaluate side-chains 129 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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: 9.9990 chunk 172 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 chunk 191 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 152 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** B 570 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 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 567 GLN G 39 GLN I 37 GLN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 40 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.042072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.034279 restraints weight = 233911.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.035188 restraints weight = 145063.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.035815 restraints weight = 102638.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.036260 restraints weight = 79703.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.036581 restraints weight = 66314.818| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 17348 Z= 0.288 Angle : 0.857 12.745 23590 Z= 0.450 Chirality : 0.048 0.278 2635 Planarity : 0.006 0.060 2987 Dihedral : 9.033 88.159 2807 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 32.22 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.32 % Favored : 91.92 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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 aren not related in a simple way. whole: -1.70 (0.18), residues: 2105 helix: -1.70 (0.30), residues: 213 sheet: -1.50 (0.19), residues: 673 loop : -0.70 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 596 TYR 0.023 0.003 TYR E 241 PHE 0.024 0.003 PHE J 98 TRP 0.024 0.004 TRP K 275 HIS 0.010 0.002 HIS F 602 Details of bonding type rmsd covalent geometry : bond 0.00589 (17302) covalent geometry : angle 0.84607 (23483) SS BOND : bond 0.00583 ( 25) SS BOND : angle 1.40512 ( 50) hydrogen bonds : bond 0.05133 ( 565) hydrogen bonds : angle 8.11643 ( 1407) Misc. bond : bond 0.00087 ( 2) link_ALPHA1-3 : bond 0.01317 ( 3) link_ALPHA1-3 : angle 2.47305 ( 9) link_ALPHA1-6 : bond 0.00589 ( 3) link_ALPHA1-6 : angle 1.87607 ( 9) link_BETA1-4 : bond 0.00494 ( 9) link_BETA1-4 : angle 1.90863 ( 27) link_NAG-ASN : bond 0.00725 ( 4) link_NAG-ASN : angle 4.31332 ( 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 162 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.586 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 225 PHE cc_start: 0.9084 (t80) cc_final: 0.8690 (t80) REVERT: C 59 TYR cc_start: 0.9444 (p90) cc_final: 0.9026 (p90) REVERT: C 86 ASP cc_start: 0.8583 (m-30) cc_final: 0.8210 (m-30) REVERT: E 51 LEU cc_start: 0.6929 (mt) cc_final: 0.6517 (mt) REVERT: F 595 GLN cc_start: 0.9449 (tm-30) cc_final: 0.8987 (tm-30) REVERT: H 73 LEU cc_start: 0.9105 (tp) cc_final: 0.8767 (tp) REVERT: H 78 LEU cc_start: 0.9670 (tp) cc_final: 0.9418 (tp) REVERT: H 79 GLN cc_start: 0.9495 (mm-40) cc_final: 0.9067 (mm-40) REVERT: H 87 PHE cc_start: 0.8281 (m-80) cc_final: 0.7893 (m-80) REVERT: H 96 PHE cc_start: 0.8571 (m-10) cc_final: 0.8365 (m-10) REVERT: I 85 ASP cc_start: 0.9436 (m-30) cc_final: 0.8993 (p0) REVERT: I 94 TYR cc_start: 0.9297 (p90) cc_final: 0.8940 (p90) REVERT: J 53 TRP cc_start: 0.8505 (t-100) cc_final: 0.8084 (t-100) REVERT: J 102 TYR cc_start: 0.8949 (t80) cc_final: 0.8401 (t80) REVERT: N 34 MET cc_start: 0.9198 (tpt) cc_final: 0.8971 (tpp) REVERT: P 73 LEU cc_start: 0.9552 (tt) cc_final: 0.9292 (tt) REVERT: Q 53 TRP cc_start: 0.7052 (m100) cc_final: 0.6659 (m100) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1174 time to fit residues: 28.8982 Evaluate side-chains 110 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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: 3.9990 chunk 56 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 205 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 150 optimal weight: 20.0000 chunk 185 optimal weight: 0.0770 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 GLN ** M 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.043616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.035719 restraints weight = 234418.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.036679 restraints weight = 142665.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.037340 restraints weight = 99275.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.037816 restraints weight = 76211.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.038150 restraints weight = 62558.265| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.5297 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= 0.194 Angle : 0.741 13.053 23590 Z= 0.387 Chirality : 0.045 0.250 2635 Planarity : 0.005 0.064 2987 Dihedral : 8.628 87.417 2807 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 24.97 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.70 % Favored : 92.59 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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 aren not related in a simple way. whole: -1.59 (0.18), residues: 2105 helix: -1.41 (0.31), residues: 205 sheet: -1.57 (0.20), residues: 621 loop : -0.63 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 302 TYR 0.018 0.002 TYR E 137 PHE 0.024 0.002 PHE C 32 TRP 0.042 0.003 TRP B 531 HIS 0.008 0.001 HIS F 602 Details of bonding type rmsd covalent geometry : bond 0.00413 (17302) covalent geometry : angle 0.73134 (23483) SS BOND : bond 0.00482 ( 25) SS BOND : angle 1.10171 ( 50) hydrogen bonds : bond 0.04443 ( 565) hydrogen bonds : angle 7.74069 ( 1407) Misc. bond : bond 0.00038 ( 2) link_ALPHA1-3 : bond 0.01232 ( 3) link_ALPHA1-3 : angle 1.84043 ( 9) link_ALPHA1-6 : bond 0.00737 ( 3) link_ALPHA1-6 : angle 1.54662 ( 9) link_BETA1-4 : bond 0.00458 ( 9) link_BETA1-4 : angle 1.76607 ( 27) link_NAG-ASN : bond 0.00376 ( 4) link_NAG-ASN : angle 4.17714 ( 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 163 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.590 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 225 PHE cc_start: 0.9079 (t80) cc_final: 0.8754 (t80) REVERT: B 585 LEU cc_start: 0.9379 (pt) cc_final: 0.8858 (pt) REVERT: C 59 TYR cc_start: 0.9456 (p90) cc_final: 0.9039 (p90) REVERT: C 82 LEU cc_start: 0.9465 (mp) cc_final: 0.9108 (mp) REVERT: E 51 LEU cc_start: 0.6978 (mt) cc_final: 0.6542 (mt) REVERT: F 595 GLN cc_start: 0.9431 (tm-30) cc_final: 0.8939 (tm-30) REVERT: G 36 TRP cc_start: 0.9510 (m100) cc_final: 0.9245 (m100) REVERT: H 73 LEU cc_start: 0.9022 (tp) cc_final: 0.8671 (tp) REVERT: H 78 LEU cc_start: 0.9654 (tp) cc_final: 0.9387 (tp) REVERT: H 79 GLN cc_start: 0.9529 (mm-40) cc_final: 0.9099 (mm-40) REVERT: H 87 PHE cc_start: 0.8309 (m-80) cc_final: 0.7959 (m-80) REVERT: I 94 TYR cc_start: 0.9316 (p90) cc_final: 0.8950 (p90) REVERT: J 53 TRP cc_start: 0.8516 (t-100) cc_final: 0.8082 (t-100) REVERT: J 102 TYR cc_start: 0.8958 (t80) cc_final: 0.8486 (t80) REVERT: N 34 MET cc_start: 0.9227 (tpt) cc_final: 0.8953 (tpp) REVERT: N 109 VAL cc_start: 0.9436 (t) cc_final: 0.8843 (t) REVERT: P 28 ASN cc_start: 0.9311 (t0) cc_final: 0.9075 (t0) REVERT: P 73 LEU cc_start: 0.9488 (tt) cc_final: 0.9182 (tt) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1218 time to fit residues: 30.0711 Evaluate side-chains 115 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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: 10.0000 chunk 179 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 162 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 ASN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN K 278 ASN ** M 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 5 GLN N 105 GLN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.040820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.033045 restraints weight = 246666.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.033949 restraints weight = 151671.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.034573 restraints weight = 106757.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.035025 restraints weight = 82699.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.035300 restraints weight = 68456.025| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 17348 Z= 0.306 Angle : 0.863 11.104 23590 Z= 0.453 Chirality : 0.048 0.270 2635 Planarity : 0.006 0.062 2987 Dihedral : 8.754 79.921 2807 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 34.42 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.07 % Favored : 90.17 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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 aren not related in a simple way. whole: -2.17 (0.18), residues: 2105 helix: -1.82 (0.30), residues: 205 sheet: -1.78 (0.18), residues: 659 loop : -1.12 (0.18), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 302 TYR 0.025 0.003 TYR E 241 PHE 0.029 0.003 PHE G 32 TRP 0.040 0.004 TRP B 531 HIS 0.008 0.002 HIS F 602 Details of bonding type rmsd covalent geometry : bond 0.00629 (17302) covalent geometry : angle 0.85297 (23483) SS BOND : bond 0.00627 ( 25) SS BOND : angle 1.46030 ( 50) hydrogen bonds : bond 0.05153 ( 565) hydrogen bonds : angle 8.13091 ( 1407) Misc. bond : bond 0.00089 ( 2) link_ALPHA1-3 : bond 0.01227 ( 3) link_ALPHA1-3 : angle 2.17692 ( 9) link_ALPHA1-6 : bond 0.00599 ( 3) link_ALPHA1-6 : angle 1.67036 ( 9) link_BETA1-4 : bond 0.00521 ( 9) link_BETA1-4 : angle 2.06817 ( 27) link_NAG-ASN : bond 0.00819 ( 4) link_NAG-ASN : angle 3.93988 ( 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 148 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.655 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: A 225 PHE cc_start: 0.9150 (t80) cc_final: 0.8805 (t80) REVERT: B 585 LEU cc_start: 0.9317 (pt) cc_final: 0.8998 (pt) REVERT: C 59 TYR cc_start: 0.9438 (p90) cc_final: 0.9152 (p90) REVERT: E 51 LEU cc_start: 0.7080 (mt) cc_final: 0.6645 (mt) REVERT: F 595 GLN cc_start: 0.9435 (tm-30) cc_final: 0.8975 (tm-30) REVERT: H 78 LEU cc_start: 0.9682 (tp) cc_final: 0.9449 (tp) REVERT: H 79 GLN cc_start: 0.9501 (mm-40) cc_final: 0.9089 (mm-40) REVERT: H 87 PHE cc_start: 0.8218 (m-80) cc_final: 0.7894 (m-80) REVERT: I 94 TYR cc_start: 0.9350 (p90) cc_final: 0.9043 (p90) REVERT: J 53 TRP cc_start: 0.8534 (t-100) cc_final: 0.8210 (t-100) REVERT: J 102 TYR cc_start: 0.9006 (t80) cc_final: 0.8388 (t80) REVERT: N 13 MET cc_start: 0.9178 (ppp) cc_final: 0.8959 (ppp) REVERT: N 34 MET cc_start: 0.9236 (tpt) cc_final: 0.8925 (tpp) REVERT: N 109 VAL cc_start: 0.9497 (t) cc_final: 0.9044 (t) REVERT: P 4 MET cc_start: 0.8014 (pmm) cc_final: 0.7460 (pmm) REVERT: P 73 LEU cc_start: 0.9560 (tt) cc_final: 0.9272 (tt) REVERT: Q 53 TRP cc_start: 0.7065 (m100) cc_final: 0.6659 (m100) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1153 time to fit residues: 26.1632 Evaluate side-chains 108 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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: 6.9990 chunk 199 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 91 optimal weight: 30.0000 chunk 158 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 170 optimal weight: 8.9990 chunk 196 optimal weight: 20.0000 chunk 152 optimal weight: 8.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN H 89 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.042328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.034557 restraints weight = 236629.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.035485 restraints weight = 145033.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.036139 restraints weight = 101547.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.036612 restraints weight = 78191.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.036943 restraints weight = 64243.348| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.5935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17348 Z= 0.202 Angle : 0.745 10.775 23590 Z= 0.387 Chirality : 0.045 0.241 2635 Planarity : 0.005 0.065 2987 Dihedral : 8.314 77.532 2807 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 25.84 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.22 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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 aren not related in a simple way. whole: -1.93 (0.18), residues: 2105 helix: -1.45 (0.32), residues: 196 sheet: -1.82 (0.19), residues: 636 loop : -0.88 (0.18), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 302 TYR 0.018 0.002 TYR E 137 PHE 0.022 0.002 PHE G 32 TRP 0.035 0.003 TRP B 531 HIS 0.008 0.001 HIS F 602 Details of bonding type rmsd covalent geometry : bond 0.00426 (17302) covalent geometry : angle 0.73566 (23483) SS BOND : bond 0.00468 ( 25) SS BOND : angle 1.31851 ( 50) hydrogen bonds : bond 0.04453 ( 565) hydrogen bonds : angle 7.74651 ( 1407) Misc. bond : bond 0.00056 ( 2) link_ALPHA1-3 : bond 0.01283 ( 3) link_ALPHA1-3 : angle 1.37323 ( 9) link_ALPHA1-6 : bond 0.00713 ( 3) link_ALPHA1-6 : angle 1.37517 ( 9) link_BETA1-4 : bond 0.00409 ( 9) link_BETA1-4 : angle 1.80843 ( 27) link_NAG-ASN : bond 0.00343 ( 4) link_NAG-ASN : angle 3.76018 ( 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 157 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.643 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: 0.9022 (mt) cc_final: 0.8496 (mt) REVERT: A 132 PHE cc_start: 0.8126 (t80) cc_final: 0.7368 (t80) REVERT: A 225 PHE cc_start: 0.9151 (t80) cc_final: 0.8782 (t80) REVERT: A 252 PHE cc_start: 0.9040 (t80) cc_final: 0.8770 (t80) REVERT: C 59 TYR cc_start: 0.9396 (p90) cc_final: 0.9055 (p90) REVERT: D 73 LEU cc_start: 0.9215 (tt) cc_final: 0.8976 (pt) REVERT: E 51 LEU cc_start: 0.7105 (mt) cc_final: 0.6578 (mt) REVERT: F 595 GLN cc_start: 0.9384 (tm-30) cc_final: 0.8891 (tm-30) REVERT: G 41 ASN cc_start: 0.9384 (m-40) cc_final: 0.9071 (p0) REVERT: G 43 LYS cc_start: 0.9673 (mmtt) cc_final: 0.9215 (pttp) REVERT: H 73 LEU cc_start: 0.9229 (tp) cc_final: 0.8984 (tp) REVERT: H 78 LEU cc_start: 0.9666 (tp) cc_final: 0.9407 (tp) REVERT: H 79 GLN cc_start: 0.9528 (mm-40) cc_final: 0.9097 (mm-40) REVERT: H 87 PHE cc_start: 0.8250 (m-80) cc_final: 0.7951 (m-80) REVERT: I 94 TYR cc_start: 0.9311 (p90) cc_final: 0.8954 (p90) REVERT: J 53 TRP cc_start: 0.8633 (t-100) cc_final: 0.8240 (t-100) REVERT: J 100 MET cc_start: 0.8932 (tpt) cc_final: 0.8596 (mmm) REVERT: J 102 TYR cc_start: 0.8965 (t80) cc_final: 0.8213 (t80) REVERT: N 34 MET cc_start: 0.9316 (tpt) cc_final: 0.9022 (tpp) REVERT: N 41 ASN cc_start: 0.7833 (p0) cc_final: 0.7447 (p0) REVERT: N 109 VAL cc_start: 0.9477 (t) cc_final: 0.8900 (t) REVERT: P 4 MET cc_start: 0.7927 (pmm) cc_final: 0.7197 (pmm) REVERT: P 28 ASN cc_start: 0.9277 (t0) cc_final: 0.9046 (t0) REVERT: P 73 LEU cc_start: 0.9573 (tt) cc_final: 0.9322 (tt) REVERT: Q 53 TRP cc_start: 0.6948 (m100) cc_final: 0.6409 (m100) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1228 time to fit residues: 29.3188 Evaluate side-chains 115 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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: 0.8980 chunk 112 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN K 221 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.042414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.034561 restraints weight = 235982.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.035502 restraints weight = 146518.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.036154 restraints weight = 102981.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.036629 restraints weight = 79199.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.036954 restraints weight = 65035.990| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17348 Z= 0.184 Angle : 0.725 10.599 23590 Z= 0.379 Chirality : 0.045 0.249 2635 Planarity : 0.005 0.064 2987 Dihedral : 8.070 78.180 2807 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 25.24 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.41 % Favored : 90.88 % Rotamer: Outliers : 0.06 % Allowed : 0.17 % Favored : 99.78 % 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 aren not related in a simple way. whole: -1.94 (0.18), residues: 2105 helix: -1.30 (0.32), residues: 205 sheet: -1.77 (0.19), residues: 648 loop : -0.93 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 302 TYR 0.018 0.002 TYR E 137 PHE 0.036 0.002 PHE G 32 TRP 0.033 0.003 TRP B 531 HIS 0.008 0.001 HIS F 602 Details of bonding type rmsd covalent geometry : bond 0.00389 (17302) covalent geometry : angle 0.71594 (23483) SS BOND : bond 0.00556 ( 25) SS BOND : angle 1.31068 ( 50) hydrogen bonds : bond 0.04342 ( 565) hydrogen bonds : angle 7.49258 ( 1407) Misc. bond : bond 0.00068 ( 2) link_ALPHA1-3 : bond 0.01177 ( 3) link_ALPHA1-3 : angle 1.36991 ( 9) link_ALPHA1-6 : bond 0.00683 ( 3) link_ALPHA1-6 : angle 1.35402 ( 9) link_BETA1-4 : bond 0.00480 ( 9) link_BETA1-4 : angle 1.81319 ( 27) link_NAG-ASN : bond 0.00311 ( 4) link_NAG-ASN : angle 3.71807 ( 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 152 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.466 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: 0.8700 (mt) cc_final: 0.8441 (mt) REVERT: A 225 PHE cc_start: 0.9149 (t80) cc_final: 0.8775 (t80) REVERT: B 548 MET cc_start: 0.8519 (mmp) cc_final: 0.8301 (tpp) REVERT: B 578 GLU cc_start: 0.9134 (pt0) cc_final: 0.8794 (pt0) REVERT: B 602 HIS cc_start: 0.9127 (t70) cc_final: 0.8807 (t70) REVERT: B 603 ILE cc_start: 0.9303 (tt) cc_final: 0.8954 (tt) REVERT: C 59 TYR cc_start: 0.9394 (p90) cc_final: 0.9050 (p90) REVERT: C 80 MET cc_start: 0.9355 (ttp) cc_final: 0.8899 (mtm) REVERT: D 73 LEU cc_start: 0.9207 (tt) cc_final: 0.8964 (pt) REVERT: E 51 LEU cc_start: 0.7001 (mt) cc_final: 0.6561 (mt) REVERT: F 595 GLN cc_start: 0.9347 (tm-30) cc_final: 0.8833 (tm-30) REVERT: G 41 ASN cc_start: 0.9386 (m-40) cc_final: 0.9068 (p0) REVERT: G 43 LYS cc_start: 0.9639 (mmtt) cc_final: 0.9152 (pttp) REVERT: H 78 LEU cc_start: 0.9650 (tp) cc_final: 0.9388 (tp) REVERT: H 79 GLN cc_start: 0.9535 (mm-40) cc_final: 0.9097 (mm-40) REVERT: H 87 PHE cc_start: 0.8224 (m-80) cc_final: 0.7912 (m-80) REVERT: I 94 TYR cc_start: 0.9270 (p90) cc_final: 0.8923 (p90) REVERT: J 27 PHE cc_start: 0.8548 (t80) cc_final: 0.8212 (t80) REVERT: J 53 TRP cc_start: 0.8677 (t-100) cc_final: 0.8277 (t-100) REVERT: J 100 MET cc_start: 0.9020 (tpt) cc_final: 0.8762 (mmm) REVERT: J 102 TYR cc_start: 0.8991 (t80) cc_final: 0.8174 (t80) REVERT: N 34 MET cc_start: 0.9316 (tpt) cc_final: 0.9008 (tpp) REVERT: N 109 VAL cc_start: 0.9460 (t) cc_final: 0.8866 (t) REVERT: P 4 MET cc_start: 0.8006 (pmm) cc_final: 0.7247 (pmm) REVERT: P 28 ASN cc_start: 0.9219 (t0) cc_final: 0.8993 (t0) REVERT: P 73 LEU cc_start: 0.9560 (tt) cc_final: 0.9291 (tt) REVERT: Q 53 TRP cc_start: 0.6938 (m100) cc_final: 0.6462 (m100) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.1257 time to fit residues: 28.8520 Evaluate side-chains 118 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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: 1.9990 chunk 165 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 78 optimal weight: 0.0870 chunk 67 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 192 optimal weight: 7.9990 chunk 133 optimal weight: 0.4980 chunk 186 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 overall best weight: 2.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN G 39 GLN ** K 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 602 HIS N 3 GLN N 105 GLN ** P 37 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 = 0.3491 r_free = 0.3491 target = 0.043734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.035724 restraints weight = 231505.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.036704 restraints weight = 142534.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.037382 restraints weight = 99713.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.037880 restraints weight = 76409.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.038219 restraints weight = 62319.336| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.6130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17348 Z= 0.142 Angle : 0.688 10.557 23590 Z= 0.357 Chirality : 0.044 0.270 2635 Planarity : 0.005 0.064 2987 Dihedral : 7.639 77.181 2807 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.60 % Favored : 91.78 % Rotamer: Outliers : 0.06 % Allowed : 0.28 % Favored : 99.67 % 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 aren not related in a simple way. whole: -1.85 (0.18), residues: 2105 helix: -1.19 (0.32), residues: 217 sheet: -1.64 (0.19), residues: 629 loop : -0.93 (0.18), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 302 TYR 0.037 0.002 TYR E 232 PHE 0.034 0.002 PHE G 32 TRP 0.030 0.002 TRP B 531 HIS 0.008 0.001 HIS F 602 Details of bonding type rmsd covalent geometry : bond 0.00306 (17302) covalent geometry : angle 0.67909 (23483) SS BOND : bond 0.00388 ( 25) SS BOND : angle 1.13863 ( 50) hydrogen bonds : bond 0.04032 ( 565) hydrogen bonds : angle 7.11838 ( 1407) Misc. bond : bond 0.00063 ( 2) link_ALPHA1-3 : bond 0.01183 ( 3) link_ALPHA1-3 : angle 1.12634 ( 9) link_ALPHA1-6 : bond 0.00684 ( 3) link_ALPHA1-6 : angle 1.31439 ( 9) link_BETA1-4 : bond 0.00488 ( 9) link_BETA1-4 : angle 1.63174 ( 27) link_NAG-ASN : bond 0.00326 ( 4) link_NAG-ASN : angle 3.75875 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2584.77 seconds wall clock time: 45 minutes 56.37 seconds (2756.37 seconds total)