Starting phenix.real_space_refine on Sun Sep 29 15:18:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9f_31030/09_2024/7e9f_31030.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9f_31030/09_2024/7e9f_31030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9f_31030/09_2024/7e9f_31030.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9f_31030/09_2024/7e9f_31030.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9f_31030/09_2024/7e9f_31030.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9f_31030/09_2024/7e9f_31030.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12591 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 249 5.49 5 S 4 5.16 5 C 7588 2.51 5 N 2468 2.21 5 O 2970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13279 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 734 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 88} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 659 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 776 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 714 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 710 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 781 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 714 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2506 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain: "J" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2600 Classifications: {'DNA': 126} Link IDs: {'rna3p': 125} Chain: "K" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1221 Unusual residues: {'ACE': 1} Classifications: {'peptide': 163, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 160} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "L" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1221 Unusual residues: {'ACE': 1} Classifications: {'peptide': 163, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 160} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 67 Time building chain proxies: 7.94, per 1000 atoms: 0.60 Number of scatterers: 13279 At special positions: 0 Unit cell: (113, 116, 116, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 P 249 15.00 O 2970 8.00 N 2468 7.00 C 7588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.2 seconds 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 10 sheets defined 55.5% alpha, 8.7% beta 117 base pairs and 202 stacking pairs defined. Time for finding SS restraints: 5.46 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.609A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.596A pdb=" N GLY A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 removed outlier: 3.745A pdb=" N ILE A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.623A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 38 removed outlier: 3.530A pdb=" N VAL C 31 " --> pdb=" O PRO C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.308A pdb=" N VAL C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 removed outlier: 3.526A pdb=" N ASP C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'D' and resid 40 through 49 Processing helix chain 'D' and resid 58 through 87 removed outlier: 3.542A pdb=" N LYS D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 105 Processing helix chain 'D' and resid 107 through 127 removed outlier: 3.872A pdb=" N LYS D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.871A pdb=" N GLY E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 130 Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.335A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 38 removed outlier: 3.595A pdb=" N VAL G 31 " --> pdb=" O PRO G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 4.336A pdb=" N VAL G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.617A pdb=" N ASN G 90 " --> pdb=" O LEU G 86 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'H' and resid 40 through 50 removed outlier: 3.580A pdb=" N ILE H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 86 Processing helix chain 'H' and resid 93 through 105 removed outlier: 3.552A pdb=" N ILE H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 126 removed outlier: 3.574A pdb=" N LYS H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER H 126 " --> pdb=" O THR H 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 30 Processing helix chain 'K' and resid 189 through 199 removed outlier: 4.403A pdb=" N ALA K 194 " --> pdb=" O GLU K 190 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 212 removed outlier: 3.596A pdb=" N ALA K 204 " --> pdb=" O GLU K 200 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU K 206 " --> pdb=" O ARG K 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR K 212 " --> pdb=" O LEU K 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 189 through 199 removed outlier: 4.402A pdb=" N ALA L 194 " --> pdb=" O GLU L 190 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR L 195 " --> pdb=" O ASP L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 212 removed outlier: 3.597A pdb=" N ALA L 204 " --> pdb=" O GLU L 200 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU L 206 " --> pdb=" O ARG L 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR L 212 " --> pdb=" O LEU L 208 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.577A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.557A pdb=" N THR B 96 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.388A pdb=" N ARG C 43 " --> pdb=" O ILE D 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.018A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'K' and resid 15 through 16 Processing sheet with id=AA8, first strand: chain 'K' and resid 146 through 149 removed outlier: 5.857A pdb=" N PHE K 146 " --> pdb=" O HIS K 59 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS K 59 " --> pdb=" O PHE K 146 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG K 148 " --> pdb=" O VAL K 57 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL K 68 " --> pdb=" O TYR K 90 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TRP K 86 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU K 74 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU K 84 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU K 85 " --> pdb=" O ALA K 139 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ALA K 139 " --> pdb=" O LEU K 85 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA K 87 " --> pdb=" O GLU K 137 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU K 137 " --> pdb=" O ALA K 87 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR K 89 " --> pdb=" O THR K 135 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR K 133 " --> pdb=" O LEU K 91 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG K 174 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU K 134 " --> pdb=" O ARG K 174 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE K 176 " --> pdb=" O LEU K 134 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N ALA K 136 " --> pdb=" O ILE K 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 15 through 16 Processing sheet with id=AB1, first strand: chain 'L' and resid 146 through 149 removed outlier: 5.857A pdb=" N PHE L 146 " --> pdb=" O HIS L 59 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS L 59 " --> pdb=" O PHE L 146 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG L 148 " --> pdb=" O VAL L 57 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL L 68 " --> pdb=" O TYR L 90 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TRP L 86 " --> pdb=" O GLN L 72 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU L 74 " --> pdb=" O GLU L 84 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU L 84 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU L 85 " --> pdb=" O ALA L 139 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA L 139 " --> pdb=" O LEU L 85 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA L 87 " --> pdb=" O GLU L 137 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU L 137 " --> pdb=" O ALA L 87 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR L 89 " --> pdb=" O THR L 135 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR L 133 " --> pdb=" O LEU L 91 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG L 174 " --> pdb=" O LEU L 132 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU L 134 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE L 176 " --> pdb=" O LEU L 134 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ALA L 136 " --> pdb=" O ILE L 176 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 304 hydrogen bonds 600 hydrogen bond angles 0 basepair planarities 117 basepair parallelities 202 stacking parallelities Total time for adding SS restraints: 4.57 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2644 1.33 - 1.45: 4127 1.45 - 1.57: 6732 1.57 - 1.69: 496 1.69 - 1.81: 6 Bond restraints: 14005 Sorted by residual: bond pdb=" C PHE G 26 " pdb=" N PRO G 27 " ideal model delta sigma weight residual 1.333 1.356 -0.022 1.01e-02 9.80e+03 4.86e+00 bond pdb=" C3' DC I 24 " pdb=" O3' DC I 24 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.80e+00 bond pdb=" C3' DG I 63 " pdb=" O3' DG I 63 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.20e+00 bond pdb=" C LEU A 65 " pdb=" N PRO A 66 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.20e-02 6.94e+03 2.05e+00 bond pdb=" C ACE K 1 " pdb=" O ACE K 1 " ideal model delta sigma weight residual 1.199 1.228 -0.029 2.00e-02 2.50e+03 2.03e+00 ... (remaining 14000 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 19382 1.91 - 3.82: 569 3.82 - 5.73: 37 5.73 - 7.64: 13 7.64 - 9.55: 6 Bond angle restraints: 20007 Sorted by residual: angle pdb=" C LYS L 28 " pdb=" N ARG L 29 " pdb=" CA ARG L 29 " ideal model delta sigma weight residual 121.54 128.73 -7.19 1.91e+00 2.74e-01 1.42e+01 angle pdb=" C LYS K 28 " pdb=" N ARG K 29 " pdb=" CA ARG K 29 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C TRP K 93 " pdb=" N PHE K 94 " pdb=" CA PHE K 94 " ideal model delta sigma weight residual 121.70 127.84 -6.14 1.80e+00 3.09e-01 1.16e+01 angle pdb=" C TRP L 93 " pdb=" N PHE L 94 " pdb=" CA PHE L 94 " ideal model delta sigma weight residual 121.70 127.81 -6.11 1.80e+00 3.09e-01 1.15e+01 angle pdb=" C3' DC I 24 " pdb=" O3' DC I 24 " pdb=" P DG I 25 " ideal model delta sigma weight residual 120.20 124.49 -4.29 1.50e+00 4.44e-01 8.20e+00 ... (remaining 20002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.38: 5977 29.38 - 58.77: 1609 58.77 - 88.15: 137 88.15 - 117.54: 1 117.54 - 146.92: 2 Dihedral angle restraints: 7726 sinusoidal: 4661 harmonic: 3065 Sorted by residual: dihedral pdb=" C4' DC I 24 " pdb=" C3' DC I 24 " pdb=" O3' DC I 24 " pdb=" P DG I 25 " ideal model delta sinusoidal sigma weight residual 220.00 73.08 146.92 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" C4' DG I 63 " pdb=" C3' DG I 63 " pdb=" O3' DG I 63 " pdb=" P DC I 64 " ideal model delta sinusoidal sigma weight residual 220.00 77.94 142.06 1 3.50e+01 8.16e-04 1.40e+01 dihedral pdb=" CA GLU B 74 " pdb=" C GLU B 74 " pdb=" N HIS B 75 " pdb=" CA HIS B 75 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 7723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1566 0.038 - 0.077: 523 0.077 - 0.115: 181 0.115 - 0.153: 38 0.153 - 0.191: 8 Chirality restraints: 2316 Sorted by residual: chirality pdb=" CB ILE F 29 " pdb=" CA ILE F 29 " pdb=" CG1 ILE F 29 " pdb=" CG2 ILE F 29 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" P DG I 25 " pdb=" OP1 DG I 25 " pdb=" OP2 DG I 25 " pdb=" O5' DG I 25 " both_signs ideal model delta sigma weight residual True 2.35 -2.54 -0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" CA ILE B 46 " pdb=" N ILE B 46 " pdb=" C ILE B 46 " pdb=" CB ILE B 46 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.84e-01 ... (remaining 2313 not shown) Planarity restraints: 1668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 31 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO F 32 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO F 32 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 32 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 65 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO E 66 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 66 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 66 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 80 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO G 81 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO G 81 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 81 " -0.028 5.00e-02 4.00e+02 ... (remaining 1665 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3030 2.79 - 3.32: 10791 3.32 - 3.85: 26708 3.85 - 4.37: 28995 4.37 - 4.90: 42896 Nonbonded interactions: 112420 Sorted by model distance: nonbonded pdb=" O2 DC I 130 " pdb=" N2 DG J 18 " model vdw 2.264 2.496 nonbonded pdb=" N2 DG I 126 " pdb=" O2 DC J 22 " model vdw 2.319 2.496 nonbonded pdb=" OG SER H 93 " pdb=" OE1 GLU H 96 " model vdw 2.369 3.040 nonbonded pdb=" OE1 GLN G 42 " pdb=" OG SER H 90 " model vdw 2.376 3.040 nonbonded pdb=" OG SER D 67 " pdb=" O GLY F 101 " model vdw 2.387 3.040 ... (remaining 112415 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' and (resid 46 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 132)) selection = (chain 'E' and (resid 46 through 80 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 82 through 132)) } ncs_group { reference = (chain 'B' and (resid 21 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 16 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 99 or (resid 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 through 116)) selection = (chain 'G' and (resid 16 through 113 or (resid 114 and (name N or name CA or nam \ e C or name O or name CB )) or resid 115 through 116)) } ncs_group { reference = (chain 'D' and (resid 35 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 127)) selection = (chain 'H' and (resid 35 through 107 or (resid 108 and (name N or name CA or nam \ e C or name O or name CB )) or resid 109 through 127)) } ncs_group { reference = chain 'K' selection = chain 'L' } 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: 0.010 Normalize map: mean=0, sd=1: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 35.480 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14005 Z= 0.210 Angle : 0.739 9.548 20007 Z= 0.436 Chirality : 0.044 0.191 2316 Planarity : 0.005 0.066 1668 Dihedral : 28.022 146.923 5742 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.36 % Allowed : 6.89 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.61 (0.18), residues: 1029 helix: -2.87 (0.14), residues: 567 sheet: -3.24 (0.54), residues: 44 loop : -3.14 (0.22), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 93 HIS 0.003 0.001 HIS F 75 PHE 0.024 0.002 PHE H 68 TYR 0.009 0.001 TYR K 40 ARG 0.003 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 377 time to evaluate : 1.200 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: A 62 ILE cc_start: 0.8660 (mt) cc_final: 0.7930 (mp) REVERT: A 79 LYS cc_start: 0.8434 (tptm) cc_final: 0.8182 (tptp) REVERT: A 92 LEU cc_start: 0.9163 (mt) cc_final: 0.8861 (tp) REVERT: B 25 ASN cc_start: 0.8257 (m-40) cc_final: 0.8037 (m110) REVERT: B 35 ARG cc_start: 0.8578 (mtp-110) cc_final: 0.8008 (ttm110) REVERT: B 37 LEU cc_start: 0.9502 (mt) cc_final: 0.9119 (mt) REVERT: B 52 GLU cc_start: 0.8229 (tp30) cc_final: 0.7969 (tp30) REVERT: B 77 LYS cc_start: 0.8849 (mttt) cc_final: 0.8512 (mttm) REVERT: C 26 PHE cc_start: 0.8908 (m-80) cc_final: 0.8344 (m-10) REVERT: C 43 ARG cc_start: 0.8717 (mtp180) cc_final: 0.8452 (mtp-110) REVERT: C 53 THR cc_start: 0.8791 (m) cc_final: 0.8570 (m) REVERT: C 96 LYS cc_start: 0.8854 (mmtm) cc_final: 0.8555 (ttmt) REVERT: D 46 LYS cc_start: 0.9348 (ttmt) cc_final: 0.9125 (ttmm) REVERT: D 79 GLU cc_start: 0.8327 (tp30) cc_final: 0.7725 (tp30) REVERT: E 54 PHE cc_start: 0.7397 (m-80) cc_final: 0.6547 (m-10) REVERT: E 69 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.7828 (ptp90) REVERT: F 40 ARG cc_start: 0.8054 (ttm170) cc_final: 0.7776 (ttt180) REVERT: F 83 SER cc_start: 0.8232 (p) cc_final: 0.8021 (m) REVERT: G 39 ASN cc_start: 0.8404 (m-40) cc_final: 0.8088 (p0) REVERT: H 43 TYR cc_start: 0.7620 (m-80) cc_final: 0.7174 (m-80) REVERT: H 46 LYS cc_start: 0.9330 (ttmt) cc_final: 0.9120 (ttmm) REVERT: H 86 TYR cc_start: 0.7918 (m-10) cc_final: 0.7561 (m-10) REVERT: K 49 LYS cc_start: 0.6236 (mtmt) cc_final: 0.5394 (mmtp) REVERT: L 49 LYS cc_start: 0.6371 (mtmt) cc_final: 0.5668 (mmtp) REVERT: L 79 LEU cc_start: 0.7380 (mt) cc_final: 0.6588 (mp) REVERT: L 134 LEU cc_start: 0.7157 (mt) cc_final: 0.6932 (tt) outliers start: 3 outliers final: 0 residues processed: 380 average time/residue: 0.3783 time to fit residues: 184.5171 Evaluate side-chains 231 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.3980 chunk 74 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 32 HIS ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 HIS F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 145 ASN L 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14005 Z= 0.231 Angle : 0.640 9.105 20007 Z= 0.362 Chirality : 0.038 0.151 2316 Planarity : 0.005 0.052 1668 Dihedral : 31.433 147.539 3864 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.32 % Allowed : 19.83 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.23), residues: 1029 helix: -0.74 (0.19), residues: 574 sheet: -2.57 (0.64), residues: 40 loop : -2.50 (0.26), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 86 HIS 0.006 0.001 HIS F 75 PHE 0.008 0.001 PHE D 68 TYR 0.017 0.001 TYR K 40 ARG 0.007 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 275 time to evaluate : 1.059 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: A 64 LYS cc_start: 0.7807 (mttt) cc_final: 0.7458 (mttm) REVERT: A 122 LYS cc_start: 0.8246 (ttpt) cc_final: 0.8004 (mmtp) REVERT: B 35 ARG cc_start: 0.8561 (mtp-110) cc_final: 0.7995 (ttm110) REVERT: B 40 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8247 (mmm-85) REVERT: B 90 LEU cc_start: 0.8898 (mt) cc_final: 0.8605 (mt) REVERT: C 43 ARG cc_start: 0.8863 (mtp180) cc_final: 0.8476 (mtp-110) REVERT: C 96 LYS cc_start: 0.8964 (mmtm) cc_final: 0.8658 (ttmt) REVERT: C 100 ASN cc_start: 0.6792 (p0) cc_final: 0.6387 (p0) REVERT: C 101 VAL cc_start: 0.9306 (t) cc_final: 0.9050 (p) REVERT: D 86 TYR cc_start: 0.8068 (m-10) cc_final: 0.7514 (m-10) REVERT: E 54 PHE cc_start: 0.7535 (m-80) cc_final: 0.6783 (m-10) REVERT: E 59 GLU cc_start: 0.8652 (pm20) cc_final: 0.8174 (pm20) REVERT: E 69 ARG cc_start: 0.8550 (mtm-85) cc_final: 0.8002 (ptp90) REVERT: E 123 ASP cc_start: 0.8435 (m-30) cc_final: 0.8186 (t0) REVERT: F 52 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7517 (tp30) REVERT: F 70 VAL cc_start: 0.8908 (t) cc_final: 0.8707 (p) REVERT: F 83 SER cc_start: 0.8177 (p) cc_final: 0.7561 (t) REVERT: H 71 ASP cc_start: 0.7887 (t70) cc_final: 0.7611 (t0) REVERT: H 86 TYR cc_start: 0.8200 (m-10) cc_final: 0.7592 (m-10) REVERT: K 49 LYS cc_start: 0.6361 (mtmt) cc_final: 0.5588 (mmtp) REVERT: L 49 LYS cc_start: 0.6524 (mtmt) cc_final: 0.5812 (mmtp) REVERT: L 148 ARG cc_start: 0.6387 (ptt-90) cc_final: 0.5917 (pmt170) outliers start: 44 outliers final: 29 residues processed: 301 average time/residue: 0.3450 time to fit residues: 135.6948 Evaluate side-chains 259 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 229 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 0.0870 chunk 78 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 115 optimal weight: 50.0000 chunk 124 optimal weight: 0.0070 chunk 102 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14005 Z= 0.213 Angle : 0.616 8.019 20007 Z= 0.350 Chirality : 0.038 0.170 2316 Planarity : 0.004 0.048 1668 Dihedral : 31.271 147.832 3864 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 6.05 % Allowed : 22.61 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.25), residues: 1029 helix: 0.18 (0.21), residues: 580 sheet: -2.04 (0.73), residues: 40 loop : -2.29 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 11 HIS 0.004 0.001 HIS F 75 PHE 0.011 0.002 PHE D 68 TYR 0.012 0.001 TYR L 40 ARG 0.007 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 257 time to evaluate : 1.235 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: A 50 GLU cc_start: 0.7460 (tt0) cc_final: 0.7255 (tt0) REVERT: A 76 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: A 97 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7515 (mm-30) REVERT: A 122 LYS cc_start: 0.8235 (ttpt) cc_final: 0.8027 (mmtt) REVERT: B 25 ASN cc_start: 0.8471 (m-40) cc_final: 0.7997 (m110) REVERT: B 77 LYS cc_start: 0.9055 (mttt) cc_final: 0.8642 (mttp) REVERT: B 90 LEU cc_start: 0.8880 (mt) cc_final: 0.8659 (mt) REVERT: B 91 LYS cc_start: 0.8896 (tttp) cc_final: 0.8632 (ptmt) REVERT: C 96 LYS cc_start: 0.8932 (mmtm) cc_final: 0.8662 (ttmt) REVERT: C 100 ASN cc_start: 0.7038 (p0) cc_final: 0.6666 (p0) REVERT: D 79 GLU cc_start: 0.8395 (tp30) cc_final: 0.7866 (tp30) REVERT: D 86 TYR cc_start: 0.8103 (m-10) cc_final: 0.7636 (m-10) REVERT: E 54 PHE cc_start: 0.7436 (m-80) cc_final: 0.6835 (m-10) REVERT: E 59 GLU cc_start: 0.8605 (pm20) cc_final: 0.8279 (pm20) REVERT: E 69 ARG cc_start: 0.8470 (mtm-85) cc_final: 0.8209 (mtp180) REVERT: E 73 GLU cc_start: 0.8010 (tt0) cc_final: 0.7179 (tt0) REVERT: E 76 GLN cc_start: 0.8628 (pt0) cc_final: 0.8419 (pt0) REVERT: E 123 ASP cc_start: 0.8511 (m-30) cc_final: 0.8187 (t0) REVERT: E 129 ARG cc_start: 0.7730 (ttt90) cc_final: 0.7371 (ttp80) REVERT: F 52 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7616 (tp30) REVERT: F 74 GLU cc_start: 0.8730 (tt0) cc_final: 0.8510 (tt0) REVERT: F 83 SER cc_start: 0.8104 (p) cc_final: 0.7492 (t) REVERT: G 26 PHE cc_start: 0.8145 (m-10) cc_final: 0.7910 (m-10) REVERT: G 59 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8479 (tp) REVERT: H 86 TYR cc_start: 0.8215 (m-10) cc_final: 0.7586 (m-10) REVERT: K 49 LYS cc_start: 0.6248 (mtmt) cc_final: 0.5439 (mmtp) REVERT: K 73 GLU cc_start: 0.7175 (mp0) cc_final: 0.6927 (pt0) REVERT: K 148 ARG cc_start: 0.6701 (ptt-90) cc_final: 0.6186 (ptt90) REVERT: L 49 LYS cc_start: 0.6477 (mtmt) cc_final: 0.5828 (mmtp) REVERT: L 148 ARG cc_start: 0.6215 (ptt-90) cc_final: 0.5828 (pmt170) REVERT: L 193 LYS cc_start: 0.8923 (mtpp) cc_final: 0.8539 (mmtp) outliers start: 50 outliers final: 35 residues processed: 288 average time/residue: 0.3551 time to fit residues: 132.6092 Evaluate side-chains 267 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 230 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 20.0000 chunk 86 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 115 optimal weight: 40.0000 chunk 122 optimal weight: 20.0000 chunk 60 optimal weight: 0.1980 chunk 109 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14005 Z= 0.223 Angle : 0.623 8.942 20007 Z= 0.352 Chirality : 0.038 0.176 2316 Planarity : 0.004 0.046 1668 Dihedral : 31.099 147.341 3864 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 6.05 % Allowed : 25.51 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.25), residues: 1029 helix: 0.61 (0.21), residues: 580 sheet: -1.95 (0.74), residues: 40 loop : -2.06 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 86 HIS 0.004 0.001 HIS F 75 PHE 0.009 0.001 PHE D 68 TYR 0.015 0.001 TYR H 43 ARG 0.010 0.001 ARG H 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 243 time to evaluate : 1.217 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: A 122 LYS cc_start: 0.8320 (ttpt) cc_final: 0.8078 (mmtt) REVERT: B 25 ASN cc_start: 0.8375 (m-40) cc_final: 0.8015 (m110) REVERT: B 35 ARG cc_start: 0.8736 (mtp-110) cc_final: 0.8394 (ttm-80) REVERT: B 77 LYS cc_start: 0.9078 (mttt) cc_final: 0.8665 (mttm) REVERT: C 96 LYS cc_start: 0.8909 (mmtm) cc_final: 0.8533 (ttpt) REVERT: C 100 ASN cc_start: 0.6938 (p0) cc_final: 0.6593 (p0) REVERT: D 79 GLU cc_start: 0.8345 (tp30) cc_final: 0.7599 (tp30) REVERT: D 88 LYS cc_start: 0.8816 (mppt) cc_final: 0.8502 (mmtt) REVERT: E 54 PHE cc_start: 0.7360 (m-80) cc_final: 0.6902 (m-10) REVERT: E 59 GLU cc_start: 0.8490 (pm20) cc_final: 0.8183 (pm20) REVERT: E 64 LYS cc_start: 0.7592 (mtpt) cc_final: 0.7200 (mttm) REVERT: E 69 ARG cc_start: 0.8491 (mtm-85) cc_final: 0.8250 (mtp180) REVERT: E 73 GLU cc_start: 0.8071 (tt0) cc_final: 0.7322 (tt0) REVERT: E 123 ASP cc_start: 0.8440 (m-30) cc_final: 0.8081 (t0) REVERT: E 129 ARG cc_start: 0.7754 (ttt90) cc_final: 0.7488 (ttp80) REVERT: F 34 ILE cc_start: 0.9414 (mm) cc_final: 0.9196 (mm) REVERT: F 52 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7662 (tp30) REVERT: F 83 SER cc_start: 0.8162 (p) cc_final: 0.7476 (t) REVERT: G 30 ARG cc_start: 0.8076 (ttm-80) cc_final: 0.7790 (ttm-80) REVERT: H 43 TYR cc_start: 0.8126 (m-80) cc_final: 0.7697 (m-80) REVERT: K 49 LYS cc_start: 0.6320 (mtmt) cc_final: 0.5508 (mmtp) REVERT: L 48 ILE cc_start: 0.6407 (mm) cc_final: 0.6087 (mp) REVERT: L 49 LYS cc_start: 0.6614 (mtmt) cc_final: 0.5977 (mmtp) REVERT: L 193 LYS cc_start: 0.8935 (mtpp) cc_final: 0.8617 (mmmt) outliers start: 50 outliers final: 37 residues processed: 272 average time/residue: 0.3475 time to fit residues: 123.4675 Evaluate side-chains 256 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 219 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 8.9990 chunk 69 optimal weight: 0.0770 chunk 1 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14005 Z= 0.369 Angle : 0.720 9.765 20007 Z= 0.399 Chirality : 0.042 0.195 2316 Planarity : 0.005 0.047 1668 Dihedral : 31.291 149.107 3864 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 7.13 % Allowed : 25.39 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.25), residues: 1029 helix: 0.42 (0.21), residues: 581 sheet: -2.09 (0.66), residues: 42 loop : -2.17 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 86 HIS 0.005 0.001 HIS F 75 PHE 0.017 0.002 PHE A 78 TYR 0.044 0.002 TYR F 88 ARG 0.009 0.001 ARG H 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 224 time to evaluate : 1.112 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: A 97 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7689 (mm-30) REVERT: A 122 LYS cc_start: 0.8449 (ttpt) cc_final: 0.8139 (mmtt) REVERT: B 44 LYS cc_start: 0.8601 (mttt) cc_final: 0.8269 (mttm) REVERT: B 46 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8734 (mm) REVERT: B 77 LYS cc_start: 0.9178 (mttt) cc_final: 0.8744 (mttp) REVERT: C 96 LYS cc_start: 0.9026 (mmtm) cc_final: 0.8684 (ttmt) REVERT: C 100 ASN cc_start: 0.6959 (p0) cc_final: 0.6592 (p0) REVERT: D 79 GLU cc_start: 0.8512 (tp30) cc_final: 0.7763 (tp30) REVERT: D 86 TYR cc_start: 0.8303 (m-10) cc_final: 0.7811 (m-80) REVERT: D 88 LYS cc_start: 0.8795 (mppt) cc_final: 0.8350 (mmtt) REVERT: D 116 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8154 (tm-30) REVERT: E 57 SER cc_start: 0.8865 (t) cc_final: 0.8563 (p) REVERT: E 59 GLU cc_start: 0.8556 (pm20) cc_final: 0.8210 (pm20) REVERT: E 69 ARG cc_start: 0.8726 (mtm-85) cc_final: 0.8391 (mtp180) REVERT: E 73 GLU cc_start: 0.8164 (tt0) cc_final: 0.7640 (tt0) REVERT: F 52 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7834 (tp30) REVERT: F 55 ARG cc_start: 0.8580 (mtt180) cc_final: 0.8341 (mtt-85) REVERT: F 83 SER cc_start: 0.8227 (p) cc_final: 0.7418 (t) REVERT: F 84 LEU cc_start: 0.8776 (tp) cc_final: 0.8528 (tp) REVERT: G 26 PHE cc_start: 0.9146 (m-10) cc_final: 0.8664 (m-10) REVERT: G 65 GLU cc_start: 0.8456 (pp20) cc_final: 0.8018 (pp20) REVERT: K 73 GLU cc_start: 0.7236 (mp0) cc_final: 0.6755 (mt-10) REVERT: L 49 LYS cc_start: 0.6699 (mtmt) cc_final: 0.5982 (mmtp) REVERT: L 73 GLU cc_start: 0.7246 (mp0) cc_final: 0.6826 (mt-10) outliers start: 59 outliers final: 45 residues processed: 266 average time/residue: 0.3232 time to fit residues: 114.1188 Evaluate side-chains 240 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 194 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 122 optimal weight: 30.0000 chunk 102 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14005 Z= 0.191 Angle : 0.621 6.912 20007 Z= 0.353 Chirality : 0.038 0.187 2316 Planarity : 0.004 0.048 1668 Dihedral : 31.039 148.317 3864 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.20 % Allowed : 28.05 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.25), residues: 1029 helix: 0.77 (0.21), residues: 580 sheet: -1.78 (0.70), residues: 42 loop : -2.03 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 86 HIS 0.003 0.001 HIS F 75 PHE 0.012 0.001 PHE D 68 TYR 0.038 0.002 TYR F 88 ARG 0.007 0.001 ARG L 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 236 time to evaluate : 1.122 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: A 122 LYS cc_start: 0.8389 (ttpt) cc_final: 0.8061 (mmtp) REVERT: B 25 ASN cc_start: 0.8394 (m-40) cc_final: 0.8034 (m110) REVERT: B 44 LYS cc_start: 0.8439 (mttt) cc_final: 0.8199 (mttm) REVERT: B 72 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7105 (t80) REVERT: C 26 PHE cc_start: 0.9221 (m-80) cc_final: 0.8893 (m-80) REVERT: C 96 LYS cc_start: 0.8974 (mmtm) cc_final: 0.8577 (ttmt) REVERT: C 100 ASN cc_start: 0.6977 (p0) cc_final: 0.6632 (p0) REVERT: D 86 TYR cc_start: 0.8193 (m-10) cc_final: 0.7160 (m-10) REVERT: D 88 LYS cc_start: 0.8712 (mppt) cc_final: 0.8409 (mmtt) REVERT: E 57 SER cc_start: 0.8758 (t) cc_final: 0.8106 (p) REVERT: E 59 GLU cc_start: 0.8473 (pm20) cc_final: 0.7891 (pm20) REVERT: E 69 ARG cc_start: 0.8570 (mtm-85) cc_final: 0.8206 (mtp180) REVERT: E 83 ARG cc_start: 0.8514 (mtp85) cc_final: 0.8309 (mtp85) REVERT: E 123 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8027 (t0) REVERT: F 52 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7488 (tp30) REVERT: F 75 HIS cc_start: 0.9108 (OUTLIER) cc_final: 0.8838 (t70) REVERT: F 83 SER cc_start: 0.8021 (p) cc_final: 0.7326 (t) REVERT: F 84 LEU cc_start: 0.8522 (tp) cc_final: 0.7565 (tp) REVERT: F 88 TYR cc_start: 0.8676 (m-80) cc_final: 0.8168 (m-80) REVERT: F 95 ARG cc_start: 0.8981 (mtm-85) cc_final: 0.8711 (mtt90) REVERT: G 26 PHE cc_start: 0.8730 (m-10) cc_final: 0.8107 (m-10) REVERT: K 73 GLU cc_start: 0.7100 (mp0) cc_final: 0.6732 (mt-10) REVERT: K 133 TYR cc_start: 0.5312 (OUTLIER) cc_final: 0.4627 (m-80) REVERT: K 148 ARG cc_start: 0.6523 (ptt-90) cc_final: 0.6291 (ptt180) REVERT: L 48 ILE cc_start: 0.6277 (mm) cc_final: 0.5943 (mp) REVERT: L 49 LYS cc_start: 0.6712 (mtmt) cc_final: 0.5988 (mmtp) REVERT: L 57 VAL cc_start: 0.7720 (OUTLIER) cc_final: 0.7468 (m) REVERT: L 73 GLU cc_start: 0.7210 (mp0) cc_final: 0.6675 (mt-10) REVERT: L 133 TYR cc_start: 0.5236 (OUTLIER) cc_final: 0.3693 (m-80) REVERT: L 174 ARG cc_start: 0.5357 (ttp-110) cc_final: 0.4346 (ptp-170) REVERT: L 193 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8555 (mmmt) outliers start: 43 outliers final: 29 residues processed: 262 average time/residue: 0.3455 time to fit residues: 118.7188 Evaluate side-chains 248 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 213 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 133 TYR Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 133 TYR Chi-restraints excluded: chain L residue 171 PHE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 30.0000 chunk 68 optimal weight: 0.7980 chunk 122 optimal weight: 0.0050 chunk 76 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 overall best weight: 2.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 HIS K 145 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14005 Z= 0.230 Angle : 0.640 8.511 20007 Z= 0.361 Chirality : 0.039 0.164 2316 Planarity : 0.004 0.047 1668 Dihedral : 31.011 148.390 3864 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.32 % Allowed : 29.26 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.25), residues: 1029 helix: 0.75 (0.21), residues: 582 sheet: -1.57 (0.74), residues: 42 loop : -1.98 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 86 HIS 0.003 0.001 HIS F 75 PHE 0.014 0.002 PHE D 68 TYR 0.033 0.002 TYR F 88 ARG 0.008 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 224 time to evaluate : 1.247 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: A 122 LYS cc_start: 0.8388 (ttpt) cc_final: 0.8104 (mmtp) REVERT: A 129 ARG cc_start: 0.7529 (ttm170) cc_final: 0.7225 (ttm170) REVERT: B 44 LYS cc_start: 0.8593 (mttt) cc_final: 0.8234 (mttm) REVERT: B 72 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7118 (t80) REVERT: B 77 LYS cc_start: 0.9078 (mttt) cc_final: 0.8645 (mttp) REVERT: B 91 LYS cc_start: 0.8896 (tttp) cc_final: 0.8514 (tttm) REVERT: C 26 PHE cc_start: 0.9241 (m-80) cc_final: 0.8857 (m-80) REVERT: C 96 LYS cc_start: 0.8984 (mmtm) cc_final: 0.8592 (ttmt) REVERT: C 100 ASN cc_start: 0.6995 (p0) cc_final: 0.6689 (p0) REVERT: D 86 TYR cc_start: 0.8137 (m-10) cc_final: 0.7207 (m-10) REVERT: D 88 LYS cc_start: 0.8736 (mppt) cc_final: 0.8302 (mmtt) REVERT: E 57 SER cc_start: 0.8715 (t) cc_final: 0.8372 (p) REVERT: E 59 GLU cc_start: 0.8350 (pm20) cc_final: 0.8070 (pm20) REVERT: E 68 GLN cc_start: 0.8450 (mt0) cc_final: 0.8109 (tt0) REVERT: E 69 ARG cc_start: 0.8581 (mtm-85) cc_final: 0.8187 (mtp180) REVERT: E 105 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7298 (tt0) REVERT: E 123 ASP cc_start: 0.8429 (m-30) cc_final: 0.8052 (t0) REVERT: F 52 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7491 (tp30) REVERT: F 75 HIS cc_start: 0.9176 (OUTLIER) cc_final: 0.8922 (t70) REVERT: F 83 SER cc_start: 0.8078 (p) cc_final: 0.7401 (t) REVERT: F 84 LEU cc_start: 0.8602 (tp) cc_final: 0.7956 (tp) REVERT: F 88 TYR cc_start: 0.8552 (m-80) cc_final: 0.8028 (m-80) REVERT: G 26 PHE cc_start: 0.8820 (m-10) cc_final: 0.8166 (m-10) REVERT: G 39 ASN cc_start: 0.8559 (m-40) cc_final: 0.8241 (p0) REVERT: K 73 GLU cc_start: 0.7014 (mp0) cc_final: 0.6369 (mt-10) REVERT: K 133 TYR cc_start: 0.5387 (OUTLIER) cc_final: 0.4697 (m-80) REVERT: K 148 ARG cc_start: 0.6287 (ptt-90) cc_final: 0.6009 (pmt170) REVERT: L 49 LYS cc_start: 0.6615 (mtmt) cc_final: 0.5892 (mmtp) REVERT: L 133 TYR cc_start: 0.5316 (OUTLIER) cc_final: 0.4702 (m-80) REVERT: L 193 LYS cc_start: 0.8868 (mtpp) cc_final: 0.8619 (mmmm) outliers start: 44 outliers final: 35 residues processed: 255 average time/residue: 0.3197 time to fit residues: 108.6644 Evaluate side-chains 247 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 207 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 133 TYR Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 133 TYR Chi-restraints excluded: chain L residue 171 PHE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 96 optimal weight: 40.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 14005 Z= 0.332 Angle : 0.700 9.982 20007 Z= 0.390 Chirality : 0.041 0.192 2316 Planarity : 0.005 0.047 1668 Dihedral : 31.128 148.919 3864 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 6.29 % Allowed : 28.90 % Favored : 64.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.25), residues: 1029 helix: 0.56 (0.21), residues: 581 sheet: -2.24 (0.86), residues: 24 loop : -2.04 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 86 HIS 0.015 0.002 HIS K 59 PHE 0.019 0.002 PHE E 67 TYR 0.026 0.002 TYR F 88 ARG 0.010 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 198 time to evaluate : 1.164 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: A 122 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8178 (mmtt) REVERT: B 44 LYS cc_start: 0.8700 (mttt) cc_final: 0.8489 (mttt) REVERT: B 77 LYS cc_start: 0.9107 (mttt) cc_final: 0.8705 (mttm) REVERT: C 96 LYS cc_start: 0.9043 (mmtm) cc_final: 0.8668 (ttmt) REVERT: D 79 GLU cc_start: 0.8489 (tp30) cc_final: 0.7734 (tp30) REVERT: D 86 TYR cc_start: 0.8237 (m-10) cc_final: 0.7666 (m-10) REVERT: D 88 LYS cc_start: 0.8688 (mppt) cc_final: 0.8349 (mmtt) REVERT: D 116 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8126 (tm-30) REVERT: E 57 SER cc_start: 0.8755 (t) cc_final: 0.8522 (t) REVERT: E 68 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: E 69 ARG cc_start: 0.8678 (mtm-85) cc_final: 0.8279 (mtp180) REVERT: E 83 ARG cc_start: 0.8605 (mtp85) cc_final: 0.8368 (mtp85) REVERT: E 105 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7297 (tt0) REVERT: E 123 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8184 (t0) REVERT: F 52 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7783 (tp30) REVERT: F 83 SER cc_start: 0.8089 (p) cc_final: 0.7426 (t) REVERT: F 84 LEU cc_start: 0.8703 (tp) cc_final: 0.8090 (tp) REVERT: F 88 TYR cc_start: 0.8661 (m-10) cc_final: 0.8242 (m-80) REVERT: G 26 PHE cc_start: 0.9050 (m-10) cc_final: 0.8387 (m-10) REVERT: G 65 GLU cc_start: 0.8274 (pp20) cc_final: 0.8014 (pp20) REVERT: K 73 GLU cc_start: 0.7094 (mp0) cc_final: 0.6888 (mp0) REVERT: K 133 TYR cc_start: 0.5494 (OUTLIER) cc_final: 0.4799 (m-80) REVERT: L 49 LYS cc_start: 0.6597 (mtmt) cc_final: 0.5898 (mmtp) REVERT: L 133 TYR cc_start: 0.5671 (OUTLIER) cc_final: 0.5015 (m-80) outliers start: 52 outliers final: 40 residues processed: 237 average time/residue: 0.3022 time to fit residues: 97.7663 Evaluate side-chains 235 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 190 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 133 TYR Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 133 TYR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 30.0000 chunk 107 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14005 Z= 0.323 Angle : 0.705 9.710 20007 Z= 0.394 Chirality : 0.041 0.221 2316 Planarity : 0.005 0.048 1668 Dihedral : 31.192 149.142 3864 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 5.93 % Allowed : 29.63 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.25), residues: 1029 helix: 0.46 (0.21), residues: 581 sheet: -2.73 (0.76), residues: 24 loop : -2.05 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 86 HIS 0.015 0.001 HIS F 75 PHE 0.013 0.002 PHE E 67 TYR 0.025 0.002 TYR F 88 ARG 0.009 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 207 time to evaluate : 1.177 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: A 122 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8176 (mmtp) REVERT: B 44 LYS cc_start: 0.8715 (mttt) cc_final: 0.8385 (mttm) REVERT: B 72 TYR cc_start: 0.8138 (OUTLIER) cc_final: 0.6912 (t80) REVERT: B 77 LYS cc_start: 0.9108 (mttt) cc_final: 0.8699 (mttp) REVERT: C 65 GLU cc_start: 0.8399 (pp20) cc_final: 0.8157 (pp20) REVERT: C 96 LYS cc_start: 0.9049 (mmtm) cc_final: 0.8670 (ttmt) REVERT: D 79 GLU cc_start: 0.8442 (tp30) cc_final: 0.7662 (tp30) REVERT: D 86 TYR cc_start: 0.8299 (m-10) cc_final: 0.7265 (m-10) REVERT: D 88 LYS cc_start: 0.8679 (mppt) cc_final: 0.8334 (mmtt) REVERT: D 116 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8131 (tm-30) REVERT: E 69 ARG cc_start: 0.8666 (mtm-85) cc_final: 0.8292 (mtp180) REVERT: E 105 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7252 (tt0) REVERT: E 123 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8282 (t0) REVERT: F 52 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7613 (tp30) REVERT: F 83 SER cc_start: 0.8055 (p) cc_final: 0.7311 (t) REVERT: F 84 LEU cc_start: 0.8673 (tp) cc_final: 0.8365 (tp) REVERT: F 95 ARG cc_start: 0.8982 (mtm-85) cc_final: 0.8707 (mtt90) REVERT: G 26 PHE cc_start: 0.9051 (m-10) cc_final: 0.8419 (m-10) REVERT: G 65 GLU cc_start: 0.8360 (pp20) cc_final: 0.8023 (pp20) REVERT: H 74 GLU cc_start: 0.7588 (tt0) cc_final: 0.7376 (tt0) REVERT: K 73 GLU cc_start: 0.7156 (mp0) cc_final: 0.6901 (mp0) REVERT: K 133 TYR cc_start: 0.5477 (OUTLIER) cc_final: 0.4786 (m-80) REVERT: L 133 TYR cc_start: 0.5718 (OUTLIER) cc_final: 0.5051 (m-80) outliers start: 49 outliers final: 41 residues processed: 243 average time/residue: 0.3123 time to fit residues: 103.4557 Evaluate side-chains 240 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 194 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 133 TYR Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 133 TYR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 100 optimal weight: 40.0000 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 61 optimal weight: 0.0970 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14005 Z= 0.290 Angle : 0.694 10.304 20007 Z= 0.388 Chirality : 0.041 0.231 2316 Planarity : 0.004 0.048 1668 Dihedral : 31.154 149.143 3864 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 5.80 % Allowed : 30.96 % Favored : 63.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1029 helix: 0.50 (0.21), residues: 581 sheet: -3.11 (0.78), residues: 20 loop : -1.98 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 86 HIS 0.014 0.001 HIS F 75 PHE 0.018 0.002 PHE D 73 TYR 0.028 0.002 TYR F 88 ARG 0.010 0.001 ARG E 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 205 time to evaluate : 1.277 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: A 122 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8179 (mmtt) REVERT: B 44 LYS cc_start: 0.8664 (mttt) cc_final: 0.8310 (mttm) REVERT: B 72 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.6956 (t80) REVERT: B 77 LYS cc_start: 0.9094 (mttt) cc_final: 0.8694 (mttp) REVERT: C 26 PHE cc_start: 0.9238 (m-80) cc_final: 0.8870 (m-80) REVERT: C 96 LYS cc_start: 0.9042 (mmtm) cc_final: 0.8657 (ttmt) REVERT: D 79 GLU cc_start: 0.8400 (tp30) cc_final: 0.7643 (tp30) REVERT: D 86 TYR cc_start: 0.8271 (m-10) cc_final: 0.7224 (m-10) REVERT: D 88 LYS cc_start: 0.8649 (mppt) cc_final: 0.8333 (mmtt) REVERT: D 116 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8109 (tm-30) REVERT: E 57 SER cc_start: 0.8755 (t) cc_final: 0.8520 (p) REVERT: E 105 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7271 (tt0) REVERT: E 123 ASP cc_start: 0.8613 (m-30) cc_final: 0.8196 (t0) REVERT: F 52 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7676 (tp30) REVERT: F 83 SER cc_start: 0.7793 (p) cc_final: 0.7072 (t) REVERT: F 84 LEU cc_start: 0.8552 (tp) cc_final: 0.8337 (tp) REVERT: F 95 ARG cc_start: 0.8908 (mtm-85) cc_final: 0.8622 (mtt90) REVERT: G 26 PHE cc_start: 0.8981 (m-10) cc_final: 0.8494 (m-10) REVERT: K 73 GLU cc_start: 0.7125 (mp0) cc_final: 0.6878 (mp0) REVERT: K 133 TYR cc_start: 0.5678 (OUTLIER) cc_final: 0.5022 (m-80) REVERT: L 133 TYR cc_start: 0.5683 (OUTLIER) cc_final: 0.4974 (m-80) outliers start: 48 outliers final: 41 residues processed: 241 average time/residue: 0.2930 time to fit residues: 96.1445 Evaluate side-chains 245 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 200 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 133 TYR Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 133 TYR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.0370 chunk 42 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.117879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.085040 restraints weight = 40238.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.086987 restraints weight = 23912.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.088247 restraints weight = 17979.365| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14005 Z= 0.196 Angle : 0.662 7.849 20007 Z= 0.372 Chirality : 0.039 0.200 2316 Planarity : 0.004 0.048 1668 Dihedral : 30.934 148.613 3864 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.51 % Allowed : 33.25 % Favored : 63.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.25), residues: 1029 helix: 0.81 (0.22), residues: 577 sheet: -2.40 (0.61), residues: 48 loop : -1.93 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 86 HIS 0.013 0.001 HIS L 59 PHE 0.018 0.001 PHE D 68 TYR 0.016 0.001 TYR F 88 ARG 0.013 0.001 ARG E 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2810.55 seconds wall clock time: 50 minutes 32.47 seconds (3032.47 seconds total)