Starting phenix.real_space_refine on Wed Mar 12 04:49:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wzx_37963/03_2025/8wzx_37963.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wzx_37963/03_2025/8wzx_37963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wzx_37963/03_2025/8wzx_37963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wzx_37963/03_2025/8wzx_37963.map" model { file = "/net/cci-nas-00/data/ceres_data/8wzx_37963/03_2025/8wzx_37963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wzx_37963/03_2025/8wzx_37963.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 4500 2.51 5 N 1400 2.21 5 O 1280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7300 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "B" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "C" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "D" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "E" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "F" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "G" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "H" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "I" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "J" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "K" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "L" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "M" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "N" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "O" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "P" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "Q" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "R" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "S" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "T" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Time building chain proxies: 5.01, per 1000 atoms: 0.69 Number of scatterers: 7300 At special positions: 0 Unit cell: (58.93, 98.77, 71.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 1280 8.00 N 1400 7.00 C 4500 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: 1.51 Conformation dependent library (CDL) restraints added in 1.0 seconds 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 100 removed outlier: 6.595A pdb=" N ASN A 97 " --> pdb=" O GLN C 98 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASN C 100 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N TRP A 99 " --> pdb=" O ASN C 100 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN C 97 " --> pdb=" O GLN E 98 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ASN E 100 " --> pdb=" O ASN C 97 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TRP C 99 " --> pdb=" O ASN E 100 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASN E 97 " --> pdb=" O GLN G 98 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN G 100 " --> pdb=" O ASN E 97 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N TRP E 99 " --> pdb=" O ASN G 100 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN G 97 " --> pdb=" O GLN I 98 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ASN I 100 " --> pdb=" O ASN G 97 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N TRP G 99 " --> pdb=" O ASN I 100 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN I 97 " --> pdb=" O GLN K 98 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ASN K 100 " --> pdb=" O ASN I 97 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TRP I 99 " --> pdb=" O ASN K 100 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASN K 97 " --> pdb=" O GLN M 98 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ASN M 100 " --> pdb=" O ASN K 97 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TRP K 99 " --> pdb=" O ASN M 100 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN M 97 " --> pdb=" O GLN O 98 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASN O 100 " --> pdb=" O ASN M 97 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TRP M 99 " --> pdb=" O ASN O 100 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN O 97 " --> pdb=" O GLN Q 98 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN Q 100 " --> pdb=" O ASN O 97 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TRP O 99 " --> pdb=" O ASN Q 100 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN Q 97 " --> pdb=" O GLN S 98 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN S 100 " --> pdb=" O ASN Q 97 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TRP Q 99 " --> pdb=" O ASN S 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 110 removed outlier: 6.591A pdb=" N LYS A 106 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N MET C 109 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASN A 108 " --> pdb=" O MET C 109 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS C 106 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N MET E 109 " --> pdb=" O LYS C 106 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASN C 108 " --> pdb=" O MET E 109 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS E 106 " --> pdb=" O THR G 107 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N MET G 109 " --> pdb=" O LYS E 106 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASN E 108 " --> pdb=" O MET G 109 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS G 106 " --> pdb=" O THR I 107 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N MET I 109 " --> pdb=" O LYS G 106 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASN G 108 " --> pdb=" O MET I 109 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS I 106 " --> pdb=" O THR K 107 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N MET K 109 " --> pdb=" O LYS I 106 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASN I 108 " --> pdb=" O MET K 109 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS K 106 " --> pdb=" O THR M 107 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N MET M 109 " --> pdb=" O LYS K 106 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASN K 108 " --> pdb=" O MET M 109 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS M 106 " --> pdb=" O THR O 107 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N MET O 109 " --> pdb=" O LYS M 106 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASN M 108 " --> pdb=" O MET O 109 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS O 106 " --> pdb=" O THR Q 107 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N MET Q 109 " --> pdb=" O LYS O 106 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASN O 108 " --> pdb=" O MET Q 109 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS Q 106 " --> pdb=" O THR S 107 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N MET S 109 " --> pdb=" O LYS Q 106 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASN Q 108 " --> pdb=" O MET S 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 118 removed outlier: 6.819A pdb=" N GLY A 114 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY C 114 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY E 114 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY G 114 " --> pdb=" O ALA I 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 123 Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.185A pdb=" N ALA A 133 " --> pdb=" O MET C 134 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA C 133 " --> pdb=" O MET E 134 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA E 133 " --> pdb=" O MET G 134 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA G 133 " --> pdb=" O MET I 134 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA I 133 " --> pdb=" O MET K 134 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA K 133 " --> pdb=" O MET M 134 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA M 133 " --> pdb=" O MET O 134 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA O 133 " --> pdb=" O MET Q 134 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ALA Q 133 " --> pdb=" O MET S 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 138 through 140 removed outlier: 6.298A pdb=" N MET A 139 " --> pdb=" O HIS C 140 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N MET C 139 " --> pdb=" O HIS E 140 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N MET E 139 " --> pdb=" O HIS G 140 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N MET G 139 " --> pdb=" O HIS I 140 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N MET I 139 " --> pdb=" O HIS K 140 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N MET K 139 " --> pdb=" O HIS M 140 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N MET M 139 " --> pdb=" O HIS O 140 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N MET O 139 " --> pdb=" O HIS Q 140 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N MET Q 139 " --> pdb=" O HIS S 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 96 through 100 removed outlier: 6.585A pdb=" N ASN B 97 " --> pdb=" O GLN D 98 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ASN D 100 " --> pdb=" O ASN B 97 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N TRP B 99 " --> pdb=" O ASN D 100 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN D 97 " --> pdb=" O GLN F 98 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ASN F 100 " --> pdb=" O ASN D 97 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N TRP D 99 " --> pdb=" O ASN F 100 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN F 97 " --> pdb=" O GLN H 98 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASN H 100 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TRP F 99 " --> pdb=" O ASN H 100 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN H 97 " --> pdb=" O GLN J 98 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN J 100 " --> pdb=" O ASN H 97 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TRP H 99 " --> pdb=" O ASN J 100 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN J 97 " --> pdb=" O GLN L 98 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ASN L 100 " --> pdb=" O ASN J 97 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TRP J 99 " --> pdb=" O ASN L 100 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN L 97 " --> pdb=" O GLN N 98 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ASN N 100 " --> pdb=" O ASN L 97 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N TRP L 99 " --> pdb=" O ASN N 100 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN N 97 " --> pdb=" O GLN P 98 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ASN P 100 " --> pdb=" O ASN N 97 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TRP N 99 " --> pdb=" O ASN P 100 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN P 97 " --> pdb=" O GLN R 98 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ASN R 100 " --> pdb=" O ASN P 97 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TRP P 99 " --> pdb=" O ASN R 100 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN R 97 " --> pdb=" O GLN T 98 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ASN T 100 " --> pdb=" O ASN R 97 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TRP R 99 " --> pdb=" O ASN T 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 106 through 110 removed outlier: 6.598A pdb=" N LYS B 106 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N MET D 109 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASN B 108 " --> pdb=" O MET D 109 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS D 106 " --> pdb=" O THR F 107 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N MET F 109 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASN D 108 " --> pdb=" O MET F 109 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS F 106 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N MET H 109 " --> pdb=" O LYS F 106 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASN F 108 " --> pdb=" O MET H 109 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS H 106 " --> pdb=" O THR J 107 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N MET J 109 " --> pdb=" O LYS H 106 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASN H 108 " --> pdb=" O MET J 109 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS J 106 " --> pdb=" O THR L 107 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N MET L 109 " --> pdb=" O LYS J 106 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ASN J 108 " --> pdb=" O MET L 109 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS L 106 " --> pdb=" O THR N 107 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N MET N 109 " --> pdb=" O LYS L 106 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASN L 108 " --> pdb=" O MET N 109 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LYS N 106 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N MET P 109 " --> pdb=" O LYS N 106 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASN N 108 " --> pdb=" O MET P 109 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS P 106 " --> pdb=" O THR R 107 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N MET R 109 " --> pdb=" O LYS P 106 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASN P 108 " --> pdb=" O MET R 109 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS R 106 " --> pdb=" O THR T 107 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N MET T 109 " --> pdb=" O LYS R 106 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASN R 108 " --> pdb=" O MET T 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.824A pdb=" N GLY F 114 " --> pdb=" O ALA H 113 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 121 through 123 Processing sheet with id=AB3, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'B' and resid 133 through 135 removed outlier: 6.198A pdb=" N ALA B 133 " --> pdb=" O MET D 134 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA D 133 " --> pdb=" O MET F 134 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA F 133 " --> pdb=" O MET H 134 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA H 133 " --> pdb=" O MET J 134 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA J 133 " --> pdb=" O MET L 134 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA L 133 " --> pdb=" O MET N 134 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ALA N 133 " --> pdb=" O MET P 134 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA P 133 " --> pdb=" O MET R 134 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ALA R 133 " --> pdb=" O MET T 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 138 through 140 removed outlier: 6.311A pdb=" N MET B 139 " --> pdb=" O HIS D 140 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N MET D 139 " --> pdb=" O HIS F 140 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N MET F 139 " --> pdb=" O HIS H 140 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N MET H 139 " --> pdb=" O HIS J 140 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N MET J 139 " --> pdb=" O HIS L 140 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N MET L 139 " --> pdb=" O HIS N 140 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N MET N 139 " --> pdb=" O HIS P 140 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N MET P 139 " --> pdb=" O HIS R 140 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N MET R 139 " --> pdb=" O HIS T 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 121 through 123 Processing sheet with id=AB7, first strand: chain 'N' and resid 121 through 123 97 hydrogen bonds defined for protein. 288 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2440 1.33 - 1.45: 963 1.45 - 1.57: 3837 1.57 - 1.68: 0 1.68 - 1.80: 240 Bond restraints: 7480 Sorted by residual: bond pdb=" C GLY E 123 " pdb=" O GLY E 123 " ideal model delta sigma weight residual 1.236 1.218 0.017 1.10e-02 8.26e+03 2.51e+00 bond pdb=" C GLY N 123 " pdb=" O GLY N 123 " ideal model delta sigma weight residual 1.236 1.219 0.017 1.10e-02 8.26e+03 2.39e+00 bond pdb=" C GLY I 123 " pdb=" O GLY I 123 " ideal model delta sigma weight residual 1.236 1.219 0.017 1.10e-02 8.26e+03 2.33e+00 bond pdb=" C GLY Q 123 " pdb=" O GLY Q 123 " ideal model delta sigma weight residual 1.236 1.219 0.017 1.10e-02 8.26e+03 2.33e+00 bond pdb=" C GLY A 123 " pdb=" O GLY A 123 " ideal model delta sigma weight residual 1.236 1.219 0.017 1.10e-02 8.26e+03 2.31e+00 ... (remaining 7475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 9422 1.55 - 3.10: 367 3.10 - 4.65: 131 4.65 - 6.20: 60 6.20 - 7.75: 20 Bond angle restraints: 10000 Sorted by residual: angle pdb=" CA LEU O 130 " pdb=" CB LEU O 130 " pdb=" CG LEU O 130 " ideal model delta sigma weight residual 116.30 124.05 -7.75 3.50e+00 8.16e-02 4.90e+00 angle pdb=" CA LEU G 130 " pdb=" CB LEU G 130 " pdb=" CG LEU G 130 " ideal model delta sigma weight residual 116.30 124.01 -7.71 3.50e+00 8.16e-02 4.85e+00 angle pdb=" CA LEU C 130 " pdb=" CB LEU C 130 " pdb=" CG LEU C 130 " ideal model delta sigma weight residual 116.30 123.98 -7.68 3.50e+00 8.16e-02 4.82e+00 angle pdb=" CA LEU L 130 " pdb=" CB LEU L 130 " pdb=" CG LEU L 130 " ideal model delta sigma weight residual 116.30 123.97 -7.67 3.50e+00 8.16e-02 4.80e+00 angle pdb=" CA LEU I 130 " pdb=" CB LEU I 130 " pdb=" CG LEU I 130 " ideal model delta sigma weight residual 116.30 123.97 -7.67 3.50e+00 8.16e-02 4.80e+00 ... (remaining 9995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.80: 3588 8.80 - 17.60: 612 17.60 - 26.40: 120 26.40 - 35.20: 20 35.20 - 44.00: 40 Dihedral angle restraints: 4380 sinusoidal: 1680 harmonic: 2700 Sorted by residual: dihedral pdb=" CA ASN S 108 " pdb=" C ASN S 108 " pdb=" N MET S 109 " pdb=" CA MET S 109 " ideal model delta harmonic sigma weight residual 180.00 166.73 13.27 0 5.00e+00 4.00e-02 7.05e+00 dihedral pdb=" CA ASN L 108 " pdb=" C ASN L 108 " pdb=" N MET L 109 " pdb=" CA MET L 109 " ideal model delta harmonic sigma weight residual 180.00 166.73 13.27 0 5.00e+00 4.00e-02 7.04e+00 dihedral pdb=" CA ASN G 108 " pdb=" C ASN G 108 " pdb=" N MET G 109 " pdb=" CA MET G 109 " ideal model delta harmonic sigma weight residual 180.00 166.74 13.26 0 5.00e+00 4.00e-02 7.04e+00 ... (remaining 4377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 541 0.036 - 0.071: 259 0.071 - 0.107: 102 0.107 - 0.142: 18 0.142 - 0.178: 40 Chirality restraints: 960 Sorted by residual: chirality pdb=" CB THR Q 95 " pdb=" CA THR Q 95 " pdb=" OG1 THR Q 95 " pdb=" CG2 THR Q 95 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.90e-01 chirality pdb=" CB THR L 95 " pdb=" CA THR L 95 " pdb=" OG1 THR L 95 " pdb=" CG2 THR L 95 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CB THR G 95 " pdb=" CA THR G 95 " pdb=" OG1 THR G 95 " pdb=" CG2 THR G 95 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.66e-01 ... (remaining 957 not shown) Planarity restraints: 1320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU L 130 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.41e+00 pdb=" C LEU L 130 " -0.021 2.00e-02 2.50e+03 pdb=" O LEU L 130 " 0.008 2.00e-02 2.50e+03 pdb=" N GLY L 131 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU M 130 " 0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C LEU M 130 " -0.020 2.00e-02 2.50e+03 pdb=" O LEU M 130 " 0.008 2.00e-02 2.50e+03 pdb=" N GLY M 131 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 130 " 0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C LEU B 130 " -0.020 2.00e-02 2.50e+03 pdb=" O LEU B 130 " 0.008 2.00e-02 2.50e+03 pdb=" N GLY B 131 " 0.007 2.00e-02 2.50e+03 ... (remaining 1317 not shown) Histogram of nonbonded interaction distances: 2.60 - 3.06: 4759 3.06 - 3.52: 7871 3.52 - 3.98: 11891 3.98 - 4.44: 15630 4.44 - 4.90: 28521 Nonbonded interactions: 68672 Sorted by model distance: nonbonded pdb=" ND1 HIS M 111 " pdb=" O PHE M 141 " model vdw 2.604 3.120 nonbonded pdb=" ND1 HIS P 111 " pdb=" O PHE P 141 " model vdw 2.604 3.120 nonbonded pdb=" ND1 HIS N 111 " pdb=" O PHE N 141 " model vdw 2.605 3.120 nonbonded pdb=" ND1 HIS G 111 " pdb=" O PHE G 141 " model vdw 2.605 3.120 nonbonded pdb=" ND1 HIS B 111 " pdb=" O PHE B 141 " model vdw 2.605 3.120 ... (remaining 68667 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.940 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:17.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 : 0.009 0.047 7480 Z= 0.655 Angle : 0.972 7.748 10000 Z= 0.461 Chirality : 0.057 0.178 960 Planarity : 0.005 0.019 1320 Dihedral : 10.359 44.003 2700 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -4.13 (0.17), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.13), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP Q 99 HIS 0.006 0.002 HIS R 96 PHE 0.018 0.005 PHE R 141 TYR 0.005 0.003 TYR H 128 ARG 0.001 0.000 ARG K 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8308 (mtpp) cc_final: 0.7907 (mptt) REVERT: B 101 LYS cc_start: 0.8615 (mtpp) cc_final: 0.7999 (mptt) REVERT: C 138 MET cc_start: 0.7655 (mtp) cc_final: 0.7442 (mtp) REVERT: D 138 MET cc_start: 0.7576 (mtp) cc_final: 0.7318 (mtt) REVERT: E 106 LYS cc_start: 0.8011 (ptpt) cc_final: 0.7408 (ptmm) REVERT: E 138 MET cc_start: 0.7618 (mtp) cc_final: 0.7342 (mtt) REVERT: F 136 ARG cc_start: 0.7605 (ttm170) cc_final: 0.7402 (ttp-170) REVERT: G 106 LYS cc_start: 0.8038 (ptpt) cc_final: 0.7487 (ptmm) REVERT: G 138 MET cc_start: 0.7457 (mtp) cc_final: 0.7069 (mtt) REVERT: H 106 LYS cc_start: 0.7777 (ptpt) cc_final: 0.7296 (ptmm) REVERT: I 106 LYS cc_start: 0.8049 (ptpt) cc_final: 0.7323 (ptmt) REVERT: O 138 MET cc_start: 0.7447 (mtp) cc_final: 0.7245 (mtp) REVERT: Q 138 MET cc_start: 0.7566 (mtp) cc_final: 0.7318 (mtt) REVERT: R 136 ARG cc_start: 0.7723 (ttm170) cc_final: 0.7499 (mtp-110) REVERT: S 138 MET cc_start: 0.7719 (mtp) cc_final: 0.7416 (mtt) outliers start: 0 outliers final: 2 residues processed: 193 average time/residue: 1.6114 time to fit residues: 323.2242 Evaluate side-chains 188 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 134 MET Chi-restraints excluded: chain H residue 143 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 ASN C 143 ASN D 97 ASN D 143 ASN E 97 ASN E 143 ASN F 143 ASN G 143 ASN I 143 ASN L 100 ASN N 143 ASN O 98 GLN O 143 ASN P 143 ASN Q 97 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.127206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.100267 restraints weight = 6473.085| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.30 r_work: 0.3268 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7480 Z= 0.207 Angle : 0.659 5.981 10000 Z= 0.302 Chirality : 0.041 0.169 960 Planarity : 0.004 0.028 1320 Dihedral : 4.612 13.999 1045 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.43 % Allowed : 14.29 % Favored : 82.29 % 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: -4.27 (0.17), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.13), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 99 HIS 0.003 0.001 HIS B 96 PHE 0.006 0.001 PHE L 141 TYR 0.003 0.001 TYR Q 128 ARG 0.008 0.001 ARG O 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8217 (mtpp) cc_final: 0.7580 (mptt) REVERT: B 101 LYS cc_start: 0.8531 (mtpp) cc_final: 0.7809 (mttt) REVERT: C 101 LYS cc_start: 0.8322 (mtpp) cc_final: 0.7655 (mttt) REVERT: D 138 MET cc_start: 0.8587 (mtp) cc_final: 0.8288 (mtt) REVERT: E 106 LYS cc_start: 0.7613 (ptpt) cc_final: 0.7093 (ptmm) REVERT: E 138 MET cc_start: 0.8642 (mtp) cc_final: 0.8412 (mtm) REVERT: F 136 ARG cc_start: 0.8248 (ttm170) cc_final: 0.7989 (ttm-80) REVERT: G 106 LYS cc_start: 0.7643 (ptpt) cc_final: 0.7044 (ptmm) REVERT: G 138 MET cc_start: 0.8370 (mtp) cc_final: 0.7888 (mtt) REVERT: H 106 LYS cc_start: 0.7524 (ptpt) cc_final: 0.7149 (ptmm) REVERT: I 106 LYS cc_start: 0.7638 (ptpt) cc_final: 0.6787 (ptmt) REVERT: M 129 MET cc_start: 0.8619 (ttp) cc_final: 0.8378 (ttt) REVERT: P 109 MET cc_start: 0.8092 (mtm) cc_final: 0.7682 (mtm) REVERT: Q 138 MET cc_start: 0.8544 (mtp) cc_final: 0.8045 (mtt) REVERT: R 136 ARG cc_start: 0.8411 (ttm170) cc_final: 0.8098 (mtm180) REVERT: S 109 MET cc_start: 0.7901 (mpt) cc_final: 0.7631 (mpt) outliers start: 24 outliers final: 0 residues processed: 197 average time/residue: 1.6611 time to fit residues: 339.9916 Evaluate side-chains 189 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 54 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 4 optimal weight: 0.0670 chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN D 97 ASN E 97 ASN E 143 ASN G 143 ASN H 97 ASN I 143 ASN N 97 ASN N 143 ASN O 97 ASN O 143 ASN R 97 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.125590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.098274 restraints weight = 6453.945| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.29 r_work: 0.3253 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7480 Z= 0.304 Angle : 0.648 5.563 10000 Z= 0.307 Chirality : 0.041 0.133 960 Planarity : 0.004 0.032 1320 Dihedral : 4.694 14.592 1040 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.57 % Allowed : 17.86 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.17), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.13), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 99 HIS 0.004 0.001 HIS B 96 PHE 0.008 0.002 PHE K 141 TYR 0.004 0.001 TYR B 128 ARG 0.007 0.001 ARG O 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8225 (mtpp) cc_final: 0.7538 (mptt) REVERT: A 129 MET cc_start: 0.7810 (ttp) cc_final: 0.7455 (tpp) REVERT: B 101 LYS cc_start: 0.8537 (mtpp) cc_final: 0.7798 (mttt) REVERT: C 101 LYS cc_start: 0.8315 (mtpp) cc_final: 0.7638 (mttt) REVERT: D 138 MET cc_start: 0.8632 (mtp) cc_final: 0.8331 (mtt) REVERT: E 106 LYS cc_start: 0.7631 (ptpt) cc_final: 0.7132 (ptmm) REVERT: E 138 MET cc_start: 0.8668 (mtp) cc_final: 0.8382 (mtt) REVERT: F 136 ARG cc_start: 0.8255 (ttm170) cc_final: 0.7977 (ttm-80) REVERT: G 106 LYS cc_start: 0.7651 (ptpt) cc_final: 0.7001 (ptmm) REVERT: G 134 MET cc_start: 0.8571 (ptp) cc_final: 0.8198 (mtm) REVERT: G 138 MET cc_start: 0.8438 (mtp) cc_final: 0.7967 (mtt) REVERT: H 106 LYS cc_start: 0.7618 (ptpt) cc_final: 0.7089 (ptmm) REVERT: I 106 LYS cc_start: 0.7688 (ptpt) cc_final: 0.6824 (ptmt) REVERT: M 129 MET cc_start: 0.8631 (ttp) cc_final: 0.8397 (ttt) REVERT: N 138 MET cc_start: 0.8401 (mtp) cc_final: 0.8092 (mtt) REVERT: P 109 MET cc_start: 0.8066 (mtm) cc_final: 0.7703 (mtm) REVERT: Q 138 MET cc_start: 0.8558 (mtp) cc_final: 0.8076 (mtt) REVERT: R 136 ARG cc_start: 0.8426 (ttm170) cc_final: 0.8098 (mtp-110) REVERT: S 109 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7672 (mpt) REVERT: S 138 MET cc_start: 0.8635 (mtp) cc_final: 0.8403 (mtt) REVERT: T 109 MET cc_start: 0.7915 (mpt) cc_final: 0.7636 (mpt) outliers start: 25 outliers final: 5 residues processed: 203 average time/residue: 2.4287 time to fit residues: 512.6020 Evaluate side-chains 201 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 195 time to evaluate : 7.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain O residue 112 MET Chi-restraints excluded: chain S residue 109 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 75 optimal weight: 0.0020 chunk 22 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN D 97 ASN D 143 ASN E 97 ASN G 143 ASN I 143 ASN J 143 ASN N 143 ASN O 98 GLN O 143 ASN P 97 ASN R 97 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.125126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.097502 restraints weight = 6382.942| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.28 r_work: 0.3271 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7480 Z= 0.263 Angle : 0.627 6.294 10000 Z= 0.294 Chirality : 0.041 0.165 960 Planarity : 0.004 0.035 1320 Dihedral : 4.569 13.747 1040 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 6.14 % Allowed : 16.57 % Favored : 77.29 % 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: -4.24 (0.17), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.13), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 99 HIS 0.003 0.001 HIS B 96 PHE 0.007 0.002 PHE L 141 TYR 0.004 0.001 TYR B 128 ARG 0.008 0.001 ARG O 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8200 (mtpp) cc_final: 0.7502 (mptt) REVERT: A 129 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7638 (tpp) REVERT: A 136 ARG cc_start: 0.8662 (ttm-80) cc_final: 0.8447 (ttm-80) REVERT: B 101 LYS cc_start: 0.8551 (mtpp) cc_final: 0.7795 (mttt) REVERT: C 101 LYS cc_start: 0.8316 (mtpp) cc_final: 0.7619 (mttt) REVERT: C 112 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7517 (tmm) REVERT: D 138 MET cc_start: 0.8608 (mtp) cc_final: 0.8299 (mtt) REVERT: E 101 LYS cc_start: 0.8530 (mtpp) cc_final: 0.7718 (mttp) REVERT: E 106 LYS cc_start: 0.7638 (ptpt) cc_final: 0.7101 (ptmm) REVERT: E 138 MET cc_start: 0.8643 (mtp) cc_final: 0.8351 (mtt) REVERT: F 97 ASN cc_start: 0.9122 (m-40) cc_final: 0.8891 (m110) REVERT: F 134 MET cc_start: 0.8458 (ptp) cc_final: 0.8230 (mtm) REVERT: F 136 ARG cc_start: 0.8231 (ttm170) cc_final: 0.7929 (ttm-80) REVERT: G 106 LYS cc_start: 0.7618 (ptpt) cc_final: 0.6982 (ptmm) REVERT: G 138 MET cc_start: 0.8386 (mtp) cc_final: 0.7908 (mtt) REVERT: H 106 LYS cc_start: 0.7630 (ptpt) cc_final: 0.7061 (ptmm) REVERT: I 106 LYS cc_start: 0.7632 (ptpt) cc_final: 0.6778 (ptmt) REVERT: I 134 MET cc_start: 0.8507 (ptp) cc_final: 0.8283 (mtm) REVERT: L 134 MET cc_start: 0.8627 (ptp) cc_final: 0.8414 (pmm) REVERT: M 129 MET cc_start: 0.8614 (ttp) cc_final: 0.8409 (ttt) REVERT: N 138 MET cc_start: 0.8430 (mtp) cc_final: 0.8123 (mtt) REVERT: P 109 MET cc_start: 0.8075 (mtm) cc_final: 0.7773 (mtm) REVERT: Q 138 MET cc_start: 0.8538 (mtp) cc_final: 0.8069 (mtt) REVERT: R 136 ARG cc_start: 0.8382 (ttm170) cc_final: 0.8087 (mtp-110) REVERT: S 109 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7653 (mpt) REVERT: S 138 MET cc_start: 0.8653 (mtp) cc_final: 0.8431 (mtt) outliers start: 43 outliers final: 8 residues processed: 213 average time/residue: 1.8540 time to fit residues: 411.5055 Evaluate side-chains 207 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 196 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain I residue 139 MET Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain N residue 112 MET Chi-restraints excluded: chain P residue 139 MET Chi-restraints excluded: chain S residue 109 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 95 optimal weight: 0.0970 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN D 97 ASN E 97 ASN F 143 ASN G 143 ASN I 143 ASN J 143 ASN N 143 ASN O 143 ASN R 97 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.126506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.099048 restraints weight = 6339.720| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.28 r_work: 0.3279 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7480 Z= 0.235 Angle : 0.640 6.814 10000 Z= 0.294 Chirality : 0.042 0.158 960 Planarity : 0.004 0.041 1320 Dihedral : 4.479 14.490 1040 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.57 % Allowed : 19.29 % Favored : 76.14 % 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: -4.19 (0.18), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.14), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 99 HIS 0.002 0.001 HIS B 96 PHE 0.006 0.001 PHE K 141 TYR 0.004 0.001 TYR B 128 ARG 0.010 0.001 ARG P 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8236 (mtpp) cc_final: 0.7543 (mptt) REVERT: A 129 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7662 (tpp) REVERT: B 101 LYS cc_start: 0.8508 (mtpp) cc_final: 0.7746 (mttt) REVERT: C 101 LYS cc_start: 0.8430 (mtpp) cc_final: 0.7747 (mttt) REVERT: C 112 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7521 (tmm) REVERT: C 136 ARG cc_start: 0.8504 (ttp-110) cc_final: 0.8146 (ttm-80) REVERT: D 138 MET cc_start: 0.8603 (mtp) cc_final: 0.8288 (mtt) REVERT: E 101 LYS cc_start: 0.8546 (mtpp) cc_final: 0.7793 (mttp) REVERT: E 106 LYS cc_start: 0.7656 (ptpt) cc_final: 0.7106 (ptmm) REVERT: E 138 MET cc_start: 0.8633 (mtp) cc_final: 0.8349 (mtt) REVERT: F 97 ASN cc_start: 0.9140 (m-40) cc_final: 0.8927 (m110) REVERT: F 134 MET cc_start: 0.8437 (ptp) cc_final: 0.8222 (mtm) REVERT: F 136 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7907 (ttm-80) REVERT: G 106 LYS cc_start: 0.7631 (ptpt) cc_final: 0.7011 (ptmm) REVERT: G 134 MET cc_start: 0.8497 (ptp) cc_final: 0.8240 (mtm) REVERT: G 138 MET cc_start: 0.8399 (mtp) cc_final: 0.7924 (mtt) REVERT: H 106 LYS cc_start: 0.7656 (ptpt) cc_final: 0.7092 (ptmm) REVERT: I 106 LYS cc_start: 0.7701 (ptpt) cc_final: 0.6779 (ptmt) REVERT: I 134 MET cc_start: 0.8512 (ptp) cc_final: 0.8174 (mtm) REVERT: K 112 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7926 (mtm) REVERT: L 134 MET cc_start: 0.8627 (ptp) cc_final: 0.8400 (pmm) REVERT: N 138 MET cc_start: 0.8386 (mtp) cc_final: 0.8082 (mtt) REVERT: Q 138 MET cc_start: 0.8527 (mtp) cc_final: 0.8064 (mtt) REVERT: R 136 ARG cc_start: 0.8369 (ttm170) cc_final: 0.8093 (mtp-110) outliers start: 32 outliers final: 8 residues processed: 210 average time/residue: 2.0124 time to fit residues: 439.0005 Evaluate side-chains 209 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain K residue 138 MET Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 112 MET Chi-restraints excluded: chain P residue 139 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 ASN E 97 ASN F 143 ASN J 143 ASN L 143 ASN N 143 ASN O 98 GLN O 143 ASN R 97 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.122829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.095136 restraints weight = 6385.406| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.27 r_work: 0.3213 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 7480 Z= 0.547 Angle : 0.772 6.699 10000 Z= 0.369 Chirality : 0.047 0.203 960 Planarity : 0.005 0.049 1320 Dihedral : 5.114 15.876 1040 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.14 % Allowed : 18.43 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.32 (0.17), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.13), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 99 HIS 0.006 0.001 HIS C 96 PHE 0.013 0.003 PHE N 141 TYR 0.008 0.002 TYR P 128 ARG 0.009 0.001 ARG O 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 0.745 Fit side-chains REVERT: A 101 LYS cc_start: 0.8326 (mtpp) cc_final: 0.7595 (mptt) REVERT: A 129 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7621 (tpp) REVERT: A 136 ARG cc_start: 0.8698 (ttm-80) cc_final: 0.8451 (ttm-80) REVERT: B 101 LYS cc_start: 0.8625 (mtpp) cc_final: 0.7840 (mptt) REVERT: B 136 ARG cc_start: 0.8820 (ttm-80) cc_final: 0.8617 (ttm110) REVERT: C 101 LYS cc_start: 0.8401 (mtpp) cc_final: 0.7697 (mttt) REVERT: D 138 MET cc_start: 0.8603 (mtp) cc_final: 0.8280 (mtt) REVERT: E 106 LYS cc_start: 0.7673 (ptpt) cc_final: 0.7117 (ptmm) REVERT: E 138 MET cc_start: 0.8661 (mtp) cc_final: 0.8386 (mtt) REVERT: F 136 ARG cc_start: 0.8325 (ttm170) cc_final: 0.8057 (ttp-170) REVERT: G 106 LYS cc_start: 0.7724 (ptpt) cc_final: 0.6890 (ptmm) REVERT: G 112 MET cc_start: 0.8457 (ptp) cc_final: 0.7724 (mtm) REVERT: G 136 ARG cc_start: 0.8395 (ttm170) cc_final: 0.7947 (mtm110) REVERT: G 138 MET cc_start: 0.8470 (mtp) cc_final: 0.8019 (mtt) REVERT: H 104 LYS cc_start: 0.8141 (mttt) cc_final: 0.7627 (mtpp) REVERT: H 106 LYS cc_start: 0.7749 (ptpt) cc_final: 0.7040 (ptmm) REVERT: H 112 MET cc_start: 0.8569 (ptp) cc_final: 0.7921 (mtp) REVERT: I 106 LYS cc_start: 0.7796 (ptpt) cc_final: 0.6816 (ptmt) REVERT: J 109 MET cc_start: 0.7991 (mtm) cc_final: 0.7666 (mtm) REVERT: J 112 MET cc_start: 0.8358 (ptp) cc_final: 0.7849 (mtm) REVERT: N 138 MET cc_start: 0.8436 (mtp) cc_final: 0.8148 (mtt) REVERT: Q 138 MET cc_start: 0.8621 (mtp) cc_final: 0.8169 (mtt) REVERT: R 136 ARG cc_start: 0.8465 (ttm170) cc_final: 0.8159 (mtp-110) REVERT: S 109 MET cc_start: 0.7800 (mpt) cc_final: 0.7360 (mpt) REVERT: S 138 MET cc_start: 0.8699 (mtp) cc_final: 0.8429 (mtt) outliers start: 36 outliers final: 10 residues processed: 202 average time/residue: 1.6267 time to fit residues: 341.4124 Evaluate side-chains 203 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain P residue 112 MET Chi-restraints excluded: chain Q residue 129 MET Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain T residue 134 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 ASN E 97 ASN E 143 ASN J 143 ASN L 143 ASN N 143 ASN O 143 ASN R 97 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.126583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.099047 restraints weight = 6306.266| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.28 r_work: 0.3268 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7480 Z= 0.226 Angle : 0.663 9.067 10000 Z= 0.302 Chirality : 0.043 0.203 960 Planarity : 0.004 0.048 1320 Dihedral : 4.545 14.960 1040 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.57 % Allowed : 20.86 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.18), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.13), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 99 HIS 0.002 0.001 HIS A 111 PHE 0.005 0.001 PHE K 141 TYR 0.004 0.001 TYR H 128 ARG 0.011 0.001 ARG O 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.826 Fit side-chains REVERT: A 101 LYS cc_start: 0.8254 (mtpp) cc_final: 0.7545 (mptt) REVERT: A 129 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7654 (tpp) REVERT: B 101 LYS cc_start: 0.8566 (mtpp) cc_final: 0.7841 (mttt) REVERT: C 101 LYS cc_start: 0.8419 (mtpp) cc_final: 0.7703 (mttt) REVERT: D 138 MET cc_start: 0.8603 (mtp) cc_final: 0.8295 (mtt) REVERT: E 101 LYS cc_start: 0.8568 (mtpp) cc_final: 0.7805 (mttp) REVERT: E 106 LYS cc_start: 0.7633 (ptpt) cc_final: 0.7080 (ptmm) REVERT: E 138 MET cc_start: 0.8621 (mtp) cc_final: 0.8401 (mtt) REVERT: F 136 ARG cc_start: 0.8241 (ttm170) cc_final: 0.7927 (ttm-80) REVERT: G 106 LYS cc_start: 0.7678 (ptpt) cc_final: 0.6984 (ptmm) REVERT: G 112 MET cc_start: 0.8367 (ptp) cc_final: 0.7595 (mtm) REVERT: G 134 MET cc_start: 0.8553 (ptp) cc_final: 0.8294 (mtm) REVERT: G 136 ARG cc_start: 0.8327 (ttm170) cc_final: 0.7854 (mtm110) REVERT: G 138 MET cc_start: 0.8389 (mtp) cc_final: 0.7928 (mtt) REVERT: H 106 LYS cc_start: 0.7824 (ptpt) cc_final: 0.7101 (ptmm) REVERT: H 138 MET cc_start: 0.8435 (mtp) cc_final: 0.8080 (mtt) REVERT: I 106 LYS cc_start: 0.7758 (ptpt) cc_final: 0.6785 (ptmt) REVERT: I 134 MET cc_start: 0.8494 (ptp) cc_final: 0.8168 (mtm) REVERT: J 109 MET cc_start: 0.7986 (mtm) cc_final: 0.7777 (mtm) REVERT: K 112 MET cc_start: 0.8274 (ptp) cc_final: 0.7947 (mtm) REVERT: N 138 MET cc_start: 0.8370 (mtp) cc_final: 0.8066 (mtt) REVERT: Q 138 MET cc_start: 0.8543 (mtp) cc_final: 0.8090 (mtt) REVERT: R 136 ARG cc_start: 0.8382 (ttm170) cc_final: 0.8110 (mtp-110) REVERT: S 109 MET cc_start: 0.7811 (mpt) cc_final: 0.7603 (mpt) outliers start: 25 outliers final: 8 residues processed: 217 average time/residue: 1.5372 time to fit residues: 347.1971 Evaluate side-chains 208 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 199 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain P residue 112 MET Chi-restraints excluded: chain T residue 134 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 32 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN D 97 ASN E 97 ASN E 143 ASN J 143 ASN L 143 ASN M 98 GLN O 98 GLN O 143 ASN R 97 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.126332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.098650 restraints weight = 6384.116| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.29 r_work: 0.3278 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7480 Z= 0.244 Angle : 0.686 9.077 10000 Z= 0.311 Chirality : 0.044 0.219 960 Planarity : 0.005 0.054 1320 Dihedral : 4.540 16.832 1040 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.71 % Allowed : 21.86 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.18), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.14), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 99 HIS 0.002 0.001 HIS B 96 PHE 0.005 0.001 PHE F 141 TYR 0.005 0.001 TYR B 128 ARG 0.012 0.001 ARG O 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.895 Fit side-chains REVERT: A 101 LYS cc_start: 0.8257 (mtpp) cc_final: 0.7558 (mptt) REVERT: A 106 LYS cc_start: 0.8039 (ptpt) cc_final: 0.7432 (ptmm) REVERT: A 129 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7660 (tpp) REVERT: B 101 LYS cc_start: 0.8537 (mtpp) cc_final: 0.7802 (mttt) REVERT: D 138 MET cc_start: 0.8595 (mtp) cc_final: 0.8293 (mtt) REVERT: E 101 LYS cc_start: 0.8566 (mtpp) cc_final: 0.7816 (mttp) REVERT: E 106 LYS cc_start: 0.7683 (ptpt) cc_final: 0.7123 (ptmm) REVERT: E 138 MET cc_start: 0.8654 (mtp) cc_final: 0.8434 (mtt) REVERT: F 136 ARG cc_start: 0.8249 (ttm170) cc_final: 0.7899 (ttm-80) REVERT: G 106 LYS cc_start: 0.7696 (ptpt) cc_final: 0.7009 (ptmm) REVERT: G 112 MET cc_start: 0.8448 (ptp) cc_final: 0.7732 (mtm) REVERT: G 134 MET cc_start: 0.8557 (ptp) cc_final: 0.8287 (mtm) REVERT: G 136 ARG cc_start: 0.8311 (ttm170) cc_final: 0.7820 (mtm110) REVERT: G 138 MET cc_start: 0.8388 (mtp) cc_final: 0.7950 (mtt) REVERT: H 106 LYS cc_start: 0.7792 (ptpt) cc_final: 0.7096 (ptmm) REVERT: H 112 MET cc_start: 0.8575 (ptp) cc_final: 0.7977 (mtm) REVERT: H 136 ARG cc_start: 0.8576 (mtp-110) cc_final: 0.8186 (mtm110) REVERT: H 138 MET cc_start: 0.8460 (mtp) cc_final: 0.8120 (mtt) REVERT: I 106 LYS cc_start: 0.7723 (ptpt) cc_final: 0.6742 (ptmt) REVERT: I 134 MET cc_start: 0.8493 (ptp) cc_final: 0.8152 (mtm) REVERT: J 109 MET cc_start: 0.7976 (mtm) cc_final: 0.7621 (mtm) REVERT: J 112 MET cc_start: 0.8391 (ptp) cc_final: 0.7963 (mtm) REVERT: K 112 MET cc_start: 0.8330 (ptp) cc_final: 0.7995 (mtm) REVERT: L 134 MET cc_start: 0.8675 (ptp) cc_final: 0.8408 (pmm) REVERT: M 112 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8043 (ptp) REVERT: N 138 MET cc_start: 0.8394 (mtp) cc_final: 0.8097 (mtt) REVERT: P 138 MET cc_start: 0.8583 (mtt) cc_final: 0.8274 (mmm) REVERT: Q 138 MET cc_start: 0.8565 (mtp) cc_final: 0.8126 (mtt) REVERT: R 136 ARG cc_start: 0.8381 (ttm170) cc_final: 0.8131 (ttp-110) REVERT: S 109 MET cc_start: 0.7822 (mpt) cc_final: 0.7584 (mpp) outliers start: 26 outliers final: 12 residues processed: 207 average time/residue: 1.6272 time to fit residues: 350.4452 Evaluate side-chains 213 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain K residue 138 MET Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain N residue 112 MET Chi-restraints excluded: chain P residue 139 MET Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain T residue 134 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 25 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 65 optimal weight: 0.3980 chunk 90 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 ASN E 97 ASN E 143 ASN J 143 ASN L 143 ASN M 108 ASN N 97 ASN O 143 ASN R 97 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.126551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.098887 restraints weight = 6362.333| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.28 r_work: 0.3273 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7480 Z= 0.250 Angle : 0.702 10.342 10000 Z= 0.316 Chirality : 0.044 0.242 960 Planarity : 0.005 0.057 1320 Dihedral : 4.531 17.621 1040 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.00 % Allowed : 22.71 % Favored : 74.29 % 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: -4.29 (0.18), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.14), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 99 HIS 0.002 0.001 HIS B 96 PHE 0.006 0.001 PHE F 141 TYR 0.005 0.001 TYR B 128 ARG 0.013 0.001 ARG O 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8283 (mtpp) cc_final: 0.7582 (mptt) REVERT: A 106 LYS cc_start: 0.8048 (ptpt) cc_final: 0.7382 (ptmm) REVERT: A 129 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7635 (tpp) REVERT: B 101 LYS cc_start: 0.8562 (mtpp) cc_final: 0.7836 (mttt) REVERT: C 101 LYS cc_start: 0.8425 (mtpp) cc_final: 0.7686 (mttt) REVERT: D 138 MET cc_start: 0.8618 (mtp) cc_final: 0.8316 (mtt) REVERT: D 139 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8811 (mtp) REVERT: E 101 LYS cc_start: 0.8567 (mtpp) cc_final: 0.7815 (mttp) REVERT: E 106 LYS cc_start: 0.7648 (ptpt) cc_final: 0.7187 (ptmm) REVERT: E 138 MET cc_start: 0.8609 (mtp) cc_final: 0.8384 (mtm) REVERT: F 136 ARG cc_start: 0.8241 (ttm170) cc_final: 0.7891 (ttm-80) REVERT: G 106 LYS cc_start: 0.7688 (ptpt) cc_final: 0.7000 (ptmm) REVERT: G 112 MET cc_start: 0.8362 (ptp) cc_final: 0.7689 (mtm) REVERT: G 134 MET cc_start: 0.8552 (ptp) cc_final: 0.8292 (mtm) REVERT: G 138 MET cc_start: 0.8418 (mtp) cc_final: 0.7969 (mtt) REVERT: H 106 LYS cc_start: 0.7802 (ptpt) cc_final: 0.7133 (ptmm) REVERT: H 112 MET cc_start: 0.8484 (ptp) cc_final: 0.7850 (mtp) REVERT: H 136 ARG cc_start: 0.8588 (mtp-110) cc_final: 0.8190 (mtm110) REVERT: H 138 MET cc_start: 0.8455 (mtp) cc_final: 0.8119 (mtt) REVERT: I 134 MET cc_start: 0.8505 (ptp) cc_final: 0.8190 (mtm) REVERT: J 109 MET cc_start: 0.7993 (mtm) cc_final: 0.7628 (mtm) REVERT: J 112 MET cc_start: 0.8390 (ptp) cc_final: 0.8037 (mtm) REVERT: K 112 MET cc_start: 0.8326 (ptp) cc_final: 0.8018 (mtm) REVERT: L 134 MET cc_start: 0.8661 (ptp) cc_final: 0.8398 (pmm) REVERT: M 112 MET cc_start: 0.8431 (ptp) cc_final: 0.8129 (ptp) REVERT: N 138 MET cc_start: 0.8416 (mtp) cc_final: 0.8121 (mtt) REVERT: P 138 MET cc_start: 0.8586 (mtt) cc_final: 0.8258 (mmm) REVERT: Q 138 MET cc_start: 0.8539 (mtp) cc_final: 0.8096 (mtt) REVERT: R 136 ARG cc_start: 0.8390 (ttm170) cc_final: 0.8060 (ttp-110) REVERT: S 109 MET cc_start: 0.7834 (mpt) cc_final: 0.7555 (mpt) outliers start: 21 outliers final: 11 residues processed: 207 average time/residue: 1.6009 time to fit residues: 344.3331 Evaluate side-chains 214 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 139 MET Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain K residue 138 MET Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain N residue 112 MET Chi-restraints excluded: chain P residue 139 MET Chi-restraints excluded: chain T residue 134 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 97 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN D 97 ASN E 97 ASN E 143 ASN F 143 ASN H 97 ASN J 143 ASN L 143 ASN M 98 GLN M 108 ASN O 143 ASN R 97 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.125127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.097319 restraints weight = 6471.289| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.29 r_work: 0.3254 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7480 Z= 0.330 Angle : 0.721 10.818 10000 Z= 0.331 Chirality : 0.044 0.222 960 Planarity : 0.005 0.056 1320 Dihedral : 4.742 15.891 1040 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.57 % Allowed : 23.29 % Favored : 74.14 % 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: -4.33 (0.18), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.13), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 99 HIS 0.003 0.001 HIS B 96 PHE 0.008 0.002 PHE F 141 TYR 0.006 0.002 TYR B 128 ARG 0.013 0.001 ARG O 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 0.796 Fit side-chains REVERT: A 101 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7551 (mptt) REVERT: A 129 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7659 (tpp) REVERT: B 101 LYS cc_start: 0.8591 (mtpp) cc_final: 0.7847 (mttt) REVERT: B 136 ARG cc_start: 0.8761 (ttm-80) cc_final: 0.8526 (ttm110) REVERT: C 101 LYS cc_start: 0.8433 (mtpp) cc_final: 0.7696 (mttt) REVERT: E 101 LYS cc_start: 0.8576 (mtpp) cc_final: 0.7807 (mttp) REVERT: E 106 LYS cc_start: 0.7709 (ptpt) cc_final: 0.7135 (ptmm) REVERT: E 138 MET cc_start: 0.8645 (mtp) cc_final: 0.8432 (mtt) REVERT: F 136 ARG cc_start: 0.8250 (ttm170) cc_final: 0.7936 (ttm-80) REVERT: G 106 LYS cc_start: 0.7684 (ptpt) cc_final: 0.7015 (ptmm) REVERT: G 112 MET cc_start: 0.8499 (ptp) cc_final: 0.7806 (mtm) REVERT: G 136 ARG cc_start: 0.8287 (ttm170) cc_final: 0.7886 (mtm110) REVERT: G 138 MET cc_start: 0.8433 (mtp) cc_final: 0.8004 (mtt) REVERT: H 104 LYS cc_start: 0.8175 (mttt) cc_final: 0.7649 (mtpp) REVERT: H 106 LYS cc_start: 0.7806 (ptpt) cc_final: 0.7064 (ptmm) REVERT: H 112 MET cc_start: 0.8615 (ptp) cc_final: 0.8008 (mtm) REVERT: I 134 MET cc_start: 0.8580 (ptp) cc_final: 0.8228 (mtm) REVERT: J 109 MET cc_start: 0.7997 (mtm) cc_final: 0.7634 (mtm) REVERT: J 112 MET cc_start: 0.8465 (ptp) cc_final: 0.8080 (mtm) REVERT: K 112 MET cc_start: 0.8390 (ptp) cc_final: 0.8049 (mtm) REVERT: L 134 MET cc_start: 0.8643 (ptp) cc_final: 0.8388 (pmm) REVERT: M 112 MET cc_start: 0.8399 (ptp) cc_final: 0.8094 (ptp) REVERT: N 138 MET cc_start: 0.8426 (mtp) cc_final: 0.8137 (mtt) REVERT: Q 138 MET cc_start: 0.8597 (mtp) cc_final: 0.8160 (mtt) REVERT: R 136 ARG cc_start: 0.8387 (ttm170) cc_final: 0.8106 (mtp-110) REVERT: S 109 MET cc_start: 0.7804 (mpt) cc_final: 0.7529 (mpt) REVERT: S 138 MET cc_start: 0.8614 (mtp) cc_final: 0.8412 (mtt) outliers start: 18 outliers final: 12 residues processed: 199 average time/residue: 1.6700 time to fit residues: 345.2131 Evaluate side-chains 211 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 198 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain K residue 138 MET Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain N residue 112 MET Chi-restraints excluded: chain P residue 139 MET Chi-restraints excluded: chain T residue 134 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 96 optimal weight: 0.1980 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 ASN E 97 ASN E 143 ASN J 100 ASN J 143 ASN L 143 ASN M 108 ASN O 143 ASN R 97 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.125600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.097775 restraints weight = 6309.466| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.28 r_work: 0.3267 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 7480 Z= 0.293 Angle : 1.048 59.191 10000 Z= 0.576 Chirality : 0.046 0.545 960 Planarity : 0.005 0.053 1320 Dihedral : 4.915 41.322 1040 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.00 % Allowed : 23.86 % Favored : 74.14 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -4.33 (0.18), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.13), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 99 HIS 0.003 0.001 HIS A 96 PHE 0.007 0.002 PHE F 141 TYR 0.006 0.001 TYR B 128 ARG 0.012 0.001 ARG O 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7210.37 seconds wall clock time: 127 minutes 9.68 seconds (7629.68 seconds total)