Starting phenix.real_space_refine on Fri Oct 10 15:45:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wzx_37963/10_2025/8wzx_37963.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wzx_37963/10_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_37963/10_2025/8wzx_37963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wzx_37963/10_2025/8wzx_37963.map" model { file = "/net/cci-nas-00/data/ceres_data/8wzx_37963/10_2025/8wzx_37963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wzx_37963/10_2025/8wzx_37963.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.86, per 1000 atoms: 0.25 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: 0.58 Conformation dependent library (CDL) restraints added in 427.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.36 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: 1.06 Time building geometry restraints manager: 0.78 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' 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: 1.620 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.570 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.930 ------------------------------------------------------------------------------- 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= 0.443 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.001 0.000 ARG K 136 TYR 0.005 0.003 TYR H 128 PHE 0.018 0.005 PHE R 141 TRP 0.006 0.002 TRP Q 99 HIS 0.006 0.002 HIS R 96 Details of bonding type rmsd covalent geometry : bond 0.00945 ( 7480) covalent geometry : angle 0.97155 (10000) hydrogen bonds : bond 0.18316 ( 97) hydrogen bonds : angle 7.87177 ( 288) *********************** 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 : 0.201 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: 0.7086 time to fit residues: 142.3015 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 : 0.211 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.127054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.100019 restraints weight = 6527.663| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.31 r_work: 0.3260 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1400 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= 0.144 Angle : 0.662 5.940 10000 Z= 0.304 Chirality : 0.041 0.157 960 Planarity : 0.004 0.027 1320 Dihedral : 4.637 13.844 1045 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.54 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.26 (0.17), 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 ARG 0.006 0.001 ARG O 136 TYR 0.004 0.001 TYR Q 128 PHE 0.006 0.001 PHE L 141 TRP 0.007 0.001 TRP R 99 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7480) covalent geometry : angle 0.66189 (10000) hydrogen bonds : bond 0.03121 ( 97) hydrogen bonds : angle 4.50876 ( 288) *********************** 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 217 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8212 (mtpp) cc_final: 0.7572 (mptt) REVERT: B 101 LYS cc_start: 0.8537 (mtpp) cc_final: 0.7817 (mttt) REVERT: C 101 LYS cc_start: 0.8311 (mtpp) cc_final: 0.7641 (mttt) REVERT: C 134 MET cc_start: 0.8446 (ptp) cc_final: 0.8185 (pmm) REVERT: D 138 MET cc_start: 0.8570 (mtp) cc_final: 0.8267 (mtt) REVERT: E 106 LYS cc_start: 0.7581 (ptpt) cc_final: 0.7059 (ptmm) REVERT: E 138 MET cc_start: 0.8646 (mtp) cc_final: 0.8417 (mtm) REVERT: F 136 ARG cc_start: 0.8243 (ttm170) cc_final: 0.7982 (ttm-80) REVERT: G 106 LYS cc_start: 0.7637 (ptpt) cc_final: 0.7037 (ptmm) REVERT: G 138 MET cc_start: 0.8371 (mtp) cc_final: 0.7890 (mtt) REVERT: H 106 LYS cc_start: 0.7515 (ptpt) cc_final: 0.7142 (ptmm) REVERT: I 106 LYS cc_start: 0.7636 (ptpt) cc_final: 0.6784 (ptmt) REVERT: M 129 MET cc_start: 0.8624 (ttp) cc_final: 0.8376 (ttt) REVERT: P 109 MET cc_start: 0.8079 (mtm) cc_final: 0.7668 (mtm) REVERT: Q 138 MET cc_start: 0.8543 (mtp) cc_final: 0.8046 (mtt) REVERT: R 136 ARG cc_start: 0.8406 (ttm170) cc_final: 0.8105 (mtm180) REVERT: S 109 MET cc_start: 0.7886 (mpt) cc_final: 0.7615 (mpt) REVERT: S 138 MET cc_start: 0.8483 (mtp) cc_final: 0.8110 (mtt) outliers start: 24 outliers final: 0 residues processed: 196 average time/residue: 0.7923 time to fit residues: 161.4555 Evaluate side-chains 188 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 9 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.125019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.097717 restraints weight = 6402.185| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.27 r_work: 0.3237 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7480 Z= 0.240 Angle : 0.667 5.517 10000 Z= 0.317 Chirality : 0.042 0.132 960 Planarity : 0.004 0.034 1320 Dihedral : 4.812 14.614 1040 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.57 % Allowed : 18.00 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.008 0.001 ARG O 136 TYR 0.005 0.001 TYR P 128 PHE 0.009 0.002 PHE L 141 TRP 0.007 0.001 TRP J 99 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 7480) covalent geometry : angle 0.66747 (10000) hydrogen bonds : bond 0.03214 ( 97) hydrogen bonds : angle 4.67740 ( 288) *********************** 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 224 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8237 (mtpp) cc_final: 0.7531 (mptt) REVERT: A 129 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7464 (tpp) REVERT: B 101 LYS cc_start: 0.8565 (mtpp) cc_final: 0.7766 (mptt) REVERT: C 101 LYS cc_start: 0.8339 (mtpp) cc_final: 0.7653 (mttt) REVERT: D 138 MET cc_start: 0.8645 (mtp) cc_final: 0.8344 (mtt) REVERT: D 143 ASN cc_start: 0.8751 (m-40) cc_final: 0.8518 (m110) REVERT: E 106 LYS cc_start: 0.7609 (ptpt) cc_final: 0.7110 (ptmm) REVERT: E 138 MET cc_start: 0.8665 (mtp) cc_final: 0.8381 (mtt) REVERT: E 143 ASN cc_start: 0.8798 (m-40) cc_final: 0.8461 (m-40) REVERT: F 134 MET cc_start: 0.8640 (ptp) cc_final: 0.7448 (ttm) REVERT: F 136 ARG cc_start: 0.8257 (ttm170) cc_final: 0.7949 (ttm-80) REVERT: G 106 LYS cc_start: 0.7633 (ptpt) cc_final: 0.6980 (ptmm) REVERT: G 138 MET cc_start: 0.8424 (mtp) cc_final: 0.7960 (mtt) REVERT: H 106 LYS cc_start: 0.7569 (ptpt) cc_final: 0.7031 (ptmm) REVERT: I 106 LYS cc_start: 0.7642 (ptpt) cc_final: 0.6771 (ptmt) REVERT: L 95 THR cc_start: 0.7903 (t) cc_final: 0.7610 (m) REVERT: M 129 MET cc_start: 0.8647 (ttp) cc_final: 0.8393 (ttt) REVERT: N 101 LYS cc_start: 0.8282 (mtpp) cc_final: 0.7917 (ttmp) REVERT: N 138 MET cc_start: 0.8401 (mtp) cc_final: 0.8097 (mtt) REVERT: P 109 MET cc_start: 0.8078 (mtm) cc_final: 0.7675 (mtm) REVERT: Q 138 MET cc_start: 0.8549 (mtp) cc_final: 0.8067 (mtt) REVERT: R 136 ARG cc_start: 0.8403 (ttm170) cc_final: 0.8105 (mtp-110) REVERT: S 109 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7620 (mpt) REVERT: T 109 MET cc_start: 0.7841 (mpt) cc_final: 0.7574 (mpt) outliers start: 25 outliers final: 7 residues processed: 202 average time/residue: 0.7893 time to fit residues: 165.6863 Evaluate side-chains 205 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 196 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 MET 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 N residue 112 MET Chi-restraints excluded: chain O residue 112 MET Chi-restraints excluded: chain P residue 139 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 86 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 G 143 ASN I 143 ASN J 143 ASN N 143 ASN 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 = 0.3798 r_free = 0.3798 target = 0.124486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.096894 restraints weight = 6485.225| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.29 r_work: 0.3236 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 7480 Z= 0.273 Angle : 0.683 5.908 10000 Z= 0.327 Chirality : 0.043 0.167 960 Planarity : 0.004 0.040 1320 Dihedral : 4.918 15.113 1040 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.57 % Allowed : 17.00 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.28 (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 ARG 0.007 0.001 ARG P 136 TYR 0.006 0.002 TYR P 128 PHE 0.010 0.002 PHE L 141 TRP 0.007 0.001 TRP C 99 HIS 0.005 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 7480) covalent geometry : angle 0.68271 (10000) hydrogen bonds : bond 0.03162 ( 97) hydrogen bonds : angle 4.76492 ( 288) *********************** 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 232 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8293 (mtpp) cc_final: 0.7553 (mptt) REVERT: A 129 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7677 (tpp) REVERT: B 101 LYS cc_start: 0.8586 (mtpp) cc_final: 0.7820 (mptt) REVERT: C 101 LYS cc_start: 0.8379 (mtpp) cc_final: 0.7692 (mttt) REVERT: C 110 LYS cc_start: 0.8400 (mtpp) cc_final: 0.8191 (mtpp) REVERT: D 138 MET cc_start: 0.8627 (mtp) cc_final: 0.8311 (mtt) REVERT: D 143 ASN cc_start: 0.8677 (m-40) cc_final: 0.8388 (m110) REVERT: E 106 LYS cc_start: 0.7639 (ptpt) cc_final: 0.7133 (ptmm) REVERT: E 138 MET cc_start: 0.8649 (mtp) cc_final: 0.8370 (mtt) REVERT: F 134 MET cc_start: 0.8620 (ptp) cc_final: 0.7496 (ttm) REVERT: G 106 LYS cc_start: 0.7713 (ptpt) cc_final: 0.7040 (ptmm) REVERT: G 138 MET cc_start: 0.8428 (mtp) cc_final: 0.7977 (mtt) REVERT: H 106 LYS cc_start: 0.7721 (ptpt) cc_final: 0.7104 (ptmm) REVERT: I 106 LYS cc_start: 0.7679 (ptpt) cc_final: 0.6723 (ptmt) REVERT: I 134 MET cc_start: 0.8539 (ptp) cc_final: 0.8234 (mtm) REVERT: I 136 ARG cc_start: 0.8494 (ttm110) cc_final: 0.8220 (ttp-110) REVERT: L 95 THR cc_start: 0.7927 (t) cc_final: 0.7602 (m) REVERT: M 129 MET cc_start: 0.8637 (ttp) cc_final: 0.8382 (ttt) REVERT: N 138 MET cc_start: 0.8422 (mtp) cc_final: 0.8129 (mtt) REVERT: P 109 MET cc_start: 0.8084 (mtm) cc_final: 0.7747 (mtm) REVERT: Q 138 MET cc_start: 0.8551 (mtp) cc_final: 0.8088 (mtt) REVERT: R 136 ARG cc_start: 0.8421 (ttm170) cc_final: 0.8147 (mtp180) REVERT: S 109 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7577 (mpt) REVERT: S 138 MET cc_start: 0.8665 (mtp) cc_final: 0.8426 (mtt) outliers start: 39 outliers final: 9 residues processed: 205 average time/residue: 0.7264 time to fit residues: 154.8795 Evaluate side-chains 204 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 193 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 I residue 139 MET Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain K residue 138 MET Chi-restraints excluded: chain N residue 112 MET Chi-restraints excluded: chain O 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 50 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 I 143 ASN J 143 ASN L 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 = 0.3805 r_free = 0.3805 target = 0.124372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.096798 restraints weight = 6474.796| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.29 r_work: 0.3234 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 7480 Z= 0.266 Angle : 0.698 6.738 10000 Z= 0.329 Chirality : 0.044 0.179 960 Planarity : 0.004 0.043 1320 Dihedral : 4.912 15.097 1040 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.71 % Allowed : 19.00 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.28 (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 ARG 0.008 0.001 ARG H 136 TYR 0.006 0.002 TYR P 128 PHE 0.009 0.002 PHE N 141 TRP 0.007 0.001 TRP D 99 HIS 0.004 0.001 HIS C 96 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 7480) covalent geometry : angle 0.69794 (10000) hydrogen bonds : bond 0.03090 ( 97) hydrogen bonds : angle 4.78033 ( 288) *********************** 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 227 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8293 (mtpp) cc_final: 0.7549 (mptt) REVERT: A 129 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7682 (tpp) REVERT: B 101 LYS cc_start: 0.8601 (mtpp) cc_final: 0.7852 (mttt) REVERT: C 101 LYS cc_start: 0.8385 (mtpp) cc_final: 0.7691 (mttt) REVERT: D 143 ASN cc_start: 0.8656 (m-40) cc_final: 0.8437 (m110) REVERT: E 106 LYS cc_start: 0.7654 (ptpt) cc_final: 0.7105 (ptmm) REVERT: E 138 MET cc_start: 0.8674 (mtp) cc_final: 0.8401 (mtt) REVERT: F 134 MET cc_start: 0.8561 (ptp) cc_final: 0.7529 (ttm) REVERT: G 106 LYS cc_start: 0.7709 (ptpt) cc_final: 0.6986 (ptmm) REVERT: G 134 MET cc_start: 0.8561 (ptp) cc_final: 0.8275 (mtm) REVERT: G 138 MET cc_start: 0.8469 (mtp) cc_final: 0.8024 (mtt) REVERT: H 104 LYS cc_start: 0.8176 (mttt) cc_final: 0.7643 (mtpp) REVERT: H 106 LYS cc_start: 0.7685 (ptpt) cc_final: 0.7031 (ptmm) REVERT: I 106 LYS cc_start: 0.7786 (ptpt) cc_final: 0.6802 (ptmt) REVERT: I 134 MET cc_start: 0.8543 (ptp) cc_final: 0.8174 (mtm) REVERT: L 95 THR cc_start: 0.7955 (t) cc_final: 0.7604 (m) REVERT: M 129 MET cc_start: 0.8619 (ttp) cc_final: 0.8364 (ttt) REVERT: N 138 MET cc_start: 0.8416 (mtp) cc_final: 0.8123 (mtt) REVERT: P 109 MET cc_start: 0.8090 (mtm) cc_final: 0.7754 (mtm) REVERT: Q 138 MET cc_start: 0.8597 (mtp) cc_final: 0.8158 (mtt) REVERT: R 136 ARG cc_start: 0.8427 (ttm170) cc_final: 0.8127 (mtp-110) REVERT: S 109 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7582 (mpt) REVERT: S 138 MET cc_start: 0.8666 (mtp) cc_final: 0.8441 (mtt) outliers start: 33 outliers final: 9 residues processed: 203 average time/residue: 0.7104 time to fit residues: 149.9136 Evaluate side-chains 204 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 193 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 O residue 112 MET Chi-restraints excluded: chain P residue 112 MET Chi-restraints excluded: chain P residue 139 MET Chi-restraints excluded: chain S residue 109 MET Chi-restraints excluded: chain T residue 107 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 64 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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 G 143 ASN I 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.124337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.096803 restraints weight = 6417.153| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.27 r_work: 0.3229 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 7480 Z= 0.287 Angle : 0.714 7.198 10000 Z= 0.337 Chirality : 0.044 0.190 960 Planarity : 0.005 0.046 1320 Dihedral : 4.949 14.922 1040 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.71 % Allowed : 20.43 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.30 (0.17), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.13), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 136 TYR 0.006 0.002 TYR P 128 PHE 0.009 0.002 PHE E 141 TRP 0.007 0.002 TRP D 99 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00597 ( 7480) covalent geometry : angle 0.71357 (10000) hydrogen bonds : bond 0.03138 ( 97) hydrogen bonds : angle 4.79148 ( 288) *********************** 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 226 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8320 (mtpp) cc_final: 0.7574 (mptt) REVERT: A 129 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7666 (tpp) REVERT: B 101 LYS cc_start: 0.8617 (mtpp) cc_final: 0.7845 (mttt) REVERT: C 101 LYS cc_start: 0.8388 (mtpp) cc_final: 0.7709 (mttt) REVERT: D 143 ASN cc_start: 0.8646 (m-40) cc_final: 0.8438 (m110) REVERT: E 106 LYS cc_start: 0.7661 (ptpt) cc_final: 0.7104 (ptmm) REVERT: E 138 MET cc_start: 0.8673 (mtp) cc_final: 0.8395 (mtt) REVERT: F 134 MET cc_start: 0.8558 (ptp) cc_final: 0.7556 (ttm) REVERT: G 106 LYS cc_start: 0.7669 (ptpt) cc_final: 0.6935 (ptmm) REVERT: G 112 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7652 (mtm) REVERT: G 138 MET cc_start: 0.8478 (mtp) cc_final: 0.8043 (mtt) REVERT: H 104 LYS cc_start: 0.8155 (mttt) cc_final: 0.7625 (mtpp) REVERT: H 106 LYS cc_start: 0.7768 (ptpt) cc_final: 0.7058 (ptmm) REVERT: I 106 LYS cc_start: 0.7792 (ptpt) cc_final: 0.6816 (ptmt) REVERT: I 134 MET cc_start: 0.8545 (ptp) cc_final: 0.8178 (mtm) REVERT: J 109 MET cc_start: 0.7933 (mtm) cc_final: 0.7716 (mtm) REVERT: J 112 MET cc_start: 0.8362 (ptp) cc_final: 0.7823 (mtm) REVERT: L 95 THR cc_start: 0.7971 (t) cc_final: 0.7606 (m) REVERT: M 129 MET cc_start: 0.8629 (ttp) cc_final: 0.8379 (ttt) REVERT: N 138 MET cc_start: 0.8434 (mtp) cc_final: 0.8140 (mtt) REVERT: P 138 MET cc_start: 0.8631 (mtt) cc_final: 0.8295 (mtp) REVERT: Q 138 MET cc_start: 0.8611 (mtp) cc_final: 0.8179 (mtt) REVERT: R 136 ARG cc_start: 0.8407 (ttm170) cc_final: 0.8068 (mtp-110) REVERT: S 109 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7563 (mpt) REVERT: S 138 MET cc_start: 0.8667 (mtp) cc_final: 0.8420 (mtt) outliers start: 33 outliers final: 11 residues processed: 202 average time/residue: 0.7611 time to fit residues: 159.8035 Evaluate side-chains 207 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 193 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 G residue 112 MET Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain L residue 134 MET Chi-restraints excluded: chain O residue 112 MET Chi-restraints excluded: chain P residue 112 MET Chi-restraints excluded: chain P residue 139 MET Chi-restraints excluded: chain S residue 109 MET Chi-restraints excluded: chain T residue 107 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 G 143 ASN I 143 ASN J 143 ASN L 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 = 0.3851 r_free = 0.3851 target = 0.127758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.100222 restraints weight = 6301.165| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.28 r_work: 0.3280 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7480 Z= 0.138 Angle : 0.643 8.852 10000 Z= 0.293 Chirality : 0.042 0.176 960 Planarity : 0.004 0.041 1320 Dihedral : 4.455 14.470 1040 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.29 % Allowed : 20.43 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.25 (0.18), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.13), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 136 TYR 0.004 0.001 TYR B 128 PHE 0.005 0.001 PHE E 141 TRP 0.007 0.001 TRP O 99 HIS 0.002 0.000 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7480) covalent geometry : angle 0.64327 (10000) hydrogen bonds : bond 0.02462 ( 97) hydrogen bonds : angle 4.41029 ( 288) *********************** 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 234 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8242 (mtpp) cc_final: 0.7561 (mptt) REVERT: A 106 LYS cc_start: 0.8023 (ptpt) cc_final: 0.7429 (ptmm) REVERT: A 129 MET cc_start: 0.7944 (ttp) cc_final: 0.7700 (tpp) REVERT: B 101 LYS cc_start: 0.8525 (mtpp) cc_final: 0.7783 (mttt) REVERT: D 143 ASN cc_start: 0.8656 (m-40) cc_final: 0.8419 (m110) REVERT: E 101 LYS cc_start: 0.8552 (mtpp) cc_final: 0.7806 (mttp) REVERT: E 106 LYS cc_start: 0.7622 (ptpt) cc_final: 0.7068 (ptmm) REVERT: E 138 MET cc_start: 0.8612 (mtp) cc_final: 0.8394 (mtt) REVERT: F 134 MET cc_start: 0.8477 (ptp) cc_final: 0.7520 (ttm) REVERT: G 106 LYS cc_start: 0.7674 (ptpt) cc_final: 0.6981 (ptmm) REVERT: G 112 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7537 (mtm) REVERT: G 134 MET cc_start: 0.8490 (ptp) cc_final: 0.8250 (mtm) REVERT: G 138 MET cc_start: 0.8408 (mtp) cc_final: 0.7975 (mtt) REVERT: H 106 LYS cc_start: 0.7790 (ptpt) cc_final: 0.7121 (ptmm) REVERT: H 112 MET cc_start: 0.8410 (ptp) cc_final: 0.7736 (mtm) REVERT: H 136 ARG cc_start: 0.8580 (mtp-110) cc_final: 0.8221 (mtm110) REVERT: H 138 MET cc_start: 0.8458 (mtp) cc_final: 0.8155 (mtt) REVERT: I 106 LYS cc_start: 0.7729 (ptpt) cc_final: 0.6749 (ptmt) REVERT: I 134 MET cc_start: 0.8491 (ptp) cc_final: 0.8169 (mtm) REVERT: J 109 MET cc_start: 0.7971 (mtm) cc_final: 0.7617 (mtm) REVERT: K 112 MET cc_start: 0.8281 (ptp) cc_final: 0.7951 (mtm) REVERT: L 134 MET cc_start: 0.8630 (ptp) cc_final: 0.8377 (pmm) REVERT: M 112 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8011 (ptp) REVERT: N 138 MET cc_start: 0.8353 (mtp) cc_final: 0.8049 (mtt) REVERT: Q 138 MET cc_start: 0.8563 (mtp) cc_final: 0.8121 (mtt) REVERT: R 136 ARG cc_start: 0.8379 (ttm170) cc_final: 0.8067 (mtp-110) outliers start: 30 outliers final: 6 residues processed: 215 average time/residue: 0.7493 time to fit residues: 167.6715 Evaluate side-chains 207 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 G residue 112 MET Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain P residue 139 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 64 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 G 143 ASN I 143 ASN J 143 ASN L 143 ASN N 97 ASN O 98 GLN O 143 ASN R 97 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.123677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.095879 restraints weight = 6478.545| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.29 r_work: 0.3226 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 7480 Z= 0.354 Angle : 0.778 7.595 10000 Z= 0.368 Chirality : 0.048 0.222 960 Planarity : 0.005 0.053 1320 Dihedral : 5.089 16.213 1040 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.71 % Allowed : 22.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.34 (0.17), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.13), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O 136 TYR 0.008 0.002 TYR B 128 PHE 0.012 0.003 PHE F 141 TRP 0.007 0.002 TRP D 99 HIS 0.005 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00739 ( 7480) covalent geometry : angle 0.77773 (10000) hydrogen bonds : bond 0.03282 ( 97) hydrogen bonds : angle 4.81683 ( 288) *********************** 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 221 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8349 (mtpp) cc_final: 0.7616 (mptt) REVERT: A 129 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7637 (tpp) REVERT: B 101 LYS cc_start: 0.8610 (mtpp) cc_final: 0.7826 (mttt) REVERT: B 136 ARG cc_start: 0.8803 (ttm-80) cc_final: 0.8583 (ttm110) REVERT: C 138 MET cc_start: 0.8647 (mtp) cc_final: 0.8409 (mtp) REVERT: E 106 LYS cc_start: 0.7694 (ptpt) cc_final: 0.7116 (ptmm) REVERT: E 138 MET cc_start: 0.8685 (mtp) cc_final: 0.8411 (mtt) REVERT: F 134 MET cc_start: 0.8557 (ptp) cc_final: 0.7550 (ttm) REVERT: G 106 LYS cc_start: 0.7674 (ptpt) cc_final: 0.6994 (ptmm) REVERT: G 112 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7735 (mtm) REVERT: G 138 MET cc_start: 0.8504 (mtp) cc_final: 0.8074 (mtt) REVERT: H 104 LYS cc_start: 0.8186 (mttt) cc_final: 0.7673 (mtpp) REVERT: H 106 LYS cc_start: 0.7760 (ptpt) cc_final: 0.7033 (ptmm) REVERT: H 112 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7957 (mtp) REVERT: I 106 LYS cc_start: 0.7746 (ptpt) cc_final: 0.6790 (ptmt) REVERT: I 134 MET cc_start: 0.8551 (ptp) cc_final: 0.8146 (mtm) REVERT: J 109 MET cc_start: 0.7961 (mtm) cc_final: 0.7619 (mtm) REVERT: J 112 MET cc_start: 0.8380 (ptp) cc_final: 0.7957 (mtm) REVERT: L 95 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7641 (m) REVERT: N 138 MET cc_start: 0.8469 (mtp) cc_final: 0.8182 (mtt) REVERT: Q 138 MET cc_start: 0.8698 (mtp) cc_final: 0.8291 (mtt) REVERT: R 136 ARG cc_start: 0.8439 (ttm170) cc_final: 0.8129 (mtp-110) REVERT: S 109 MET cc_start: 0.7800 (mpt) cc_final: 0.7580 (mpp) REVERT: S 138 MET cc_start: 0.8694 (mtp) cc_final: 0.8418 (mtt) outliers start: 26 outliers final: 13 residues processed: 202 average time/residue: 0.7808 time to fit residues: 163.8210 Evaluate side-chains 211 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 E residue 143 ASN Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain G residue 112 MET Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 139 MET 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 L residue 134 MET Chi-restraints excluded: chain P residue 139 MET Chi-restraints excluded: chain T residue 107 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 ASN D 143 ASN E 97 ASN E 143 ASN G 143 ASN I 143 ASN J 143 ASN L 143 ASN M 108 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 = 0.3859 r_free = 0.3859 target = 0.127566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.099738 restraints weight = 6237.556| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.28 r_work: 0.3288 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7480 Z= 0.136 Angle : 0.684 10.699 10000 Z= 0.307 Chirality : 0.043 0.223 960 Planarity : 0.005 0.055 1320 Dihedral : 4.520 14.929 1040 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.71 % Allowed : 23.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.013 0.001 ARG O 136 TYR 0.005 0.001 TYR J 128 PHE 0.005 0.001 PHE F 141 TRP 0.008 0.001 TRP O 99 HIS 0.002 0.000 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7480) covalent geometry : angle 0.68426 (10000) hydrogen bonds : bond 0.02423 ( 97) hydrogen bonds : angle 4.43727 ( 288) *********************** 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 222 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8294 (mtpp) cc_final: 0.7591 (mptt) REVERT: A 129 MET cc_start: 0.7880 (ttp) cc_final: 0.7634 (tpp) REVERT: B 101 LYS cc_start: 0.8556 (mtpp) cc_final: 0.7829 (mttt) REVERT: E 101 LYS cc_start: 0.8574 (mtpp) cc_final: 0.7827 (mttp) REVERT: E 106 LYS cc_start: 0.7620 (ptpt) cc_final: 0.7056 (ptmm) REVERT: E 138 MET cc_start: 0.8588 (mtp) cc_final: 0.8376 (mtm) REVERT: F 134 MET cc_start: 0.8416 (ptp) cc_final: 0.7489 (ttm) REVERT: G 97 ASN cc_start: 0.9115 (m-40) cc_final: 0.8902 (m110) REVERT: G 106 LYS cc_start: 0.7648 (ptpt) cc_final: 0.6951 (ptmm) REVERT: G 112 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7575 (mtm) REVERT: G 134 MET cc_start: 0.8491 (ptp) cc_final: 0.8255 (mtm) REVERT: G 138 MET cc_start: 0.8479 (mtp) cc_final: 0.8039 (mtt) REVERT: H 106 LYS cc_start: 0.7826 (ptpt) cc_final: 0.7134 (ptmm) REVERT: H 136 ARG cc_start: 0.8532 (mtp-110) cc_final: 0.8163 (mtm110) REVERT: H 138 MET cc_start: 0.8426 (mtp) cc_final: 0.8130 (mtt) REVERT: I 106 LYS cc_start: 0.7763 (ptpt) cc_final: 0.6779 (ptmt) REVERT: I 134 MET cc_start: 0.8502 (ptp) cc_final: 0.8181 (mtm) REVERT: K 112 MET cc_start: 0.8309 (ptp) cc_final: 0.7980 (mtm) REVERT: L 95 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7557 (m) REVERT: L 134 MET cc_start: 0.8606 (ptp) cc_final: 0.8336 (pmm) REVERT: M 112 MET cc_start: 0.8408 (ptp) cc_final: 0.8067 (ptp) REVERT: M 134 MET cc_start: 0.8599 (ptp) cc_final: 0.8388 (mtm) REVERT: N 138 MET cc_start: 0.8369 (mtp) cc_final: 0.8066 (mtt) REVERT: P 138 MET cc_start: 0.8501 (mtt) cc_final: 0.8229 (mmm) REVERT: Q 138 MET cc_start: 0.8572 (mtp) cc_final: 0.8145 (mtt) REVERT: R 136 ARG cc_start: 0.8352 (ttm170) cc_final: 0.8091 (mtp-110) REVERT: S 109 MET cc_start: 0.7806 (mpt) cc_final: 0.7507 (mpt) outliers start: 19 outliers final: 8 residues processed: 206 average time/residue: 0.7725 time to fit residues: 165.3510 Evaluate side-chains 212 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 G residue 112 MET Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain P residue 139 MET Chi-restraints excluded: chain T residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 96 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 F 143 ASN H 97 ASN L 143 ASN M 108 ASN O 98 GLN R 97 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.126214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.098602 restraints weight = 6352.720| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.28 r_work: 0.3278 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7480 Z= 0.188 Angle : 0.699 9.517 10000 Z= 0.321 Chirality : 0.043 0.226 960 Planarity : 0.005 0.059 1320 Dihedral : 4.651 14.812 1040 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.00 % Allowed : 24.14 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.30 (0.18), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.14), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG O 136 TYR 0.005 0.001 TYR B 128 PHE 0.007 0.002 PHE E 141 TRP 0.008 0.001 TRP O 99 HIS 0.002 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 7480) covalent geometry : angle 0.69915 (10000) hydrogen bonds : bond 0.02646 ( 97) hydrogen bonds : angle 4.53711 ( 288) ********************** 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 215 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7582 (mptt) REVERT: A 129 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7697 (tpp) REVERT: B 101 LYS cc_start: 0.8577 (mtpp) cc_final: 0.7833 (mttt) REVERT: C 138 MET cc_start: 0.8591 (mtp) cc_final: 0.8364 (mtp) REVERT: E 101 LYS cc_start: 0.8567 (mtpp) cc_final: 0.7808 (mttp) REVERT: E 106 LYS cc_start: 0.7676 (ptpt) cc_final: 0.7112 (ptmm) REVERT: E 138 MET cc_start: 0.8660 (mtp) cc_final: 0.8459 (mtm) REVERT: F 134 MET cc_start: 0.8524 (ptp) cc_final: 0.7566 (ttm) REVERT: G 106 LYS cc_start: 0.7677 (ptpt) cc_final: 0.6991 (ptmm) REVERT: G 112 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7679 (mtm) REVERT: G 134 MET cc_start: 0.8547 (ptp) cc_final: 0.8281 (mtm) REVERT: G 138 MET cc_start: 0.8467 (mtp) cc_final: 0.8043 (mtt) REVERT: H 106 LYS cc_start: 0.7800 (ptpt) cc_final: 0.7095 (ptmm) REVERT: H 112 MET cc_start: 0.8576 (ptp) cc_final: 0.7940 (mtp) REVERT: H 136 ARG cc_start: 0.8565 (mtp-110) cc_final: 0.8195 (mtm110) REVERT: H 138 MET cc_start: 0.8540 (mtp) cc_final: 0.8242 (mtt) REVERT: I 106 LYS cc_start: 0.7712 (ptpt) cc_final: 0.6744 (ptmt) REVERT: I 134 MET cc_start: 0.8501 (ptp) cc_final: 0.8178 (mtm) REVERT: I 139 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8762 (ttp) REVERT: J 112 MET cc_start: 0.8418 (ptp) cc_final: 0.8055 (mtm) REVERT: K 112 MET cc_start: 0.8377 (ptp) cc_final: 0.8036 (mtm) REVERT: L 95 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7568 (m) REVERT: M 112 MET cc_start: 0.8413 (ptp) cc_final: 0.8067 (ptp) REVERT: N 138 MET cc_start: 0.8419 (mtp) cc_final: 0.8129 (mtt) REVERT: P 138 MET cc_start: 0.8598 (mtt) cc_final: 0.8329 (mmm) REVERT: Q 138 MET cc_start: 0.8620 (mtp) cc_final: 0.8200 (mtt) REVERT: R 136 ARG cc_start: 0.8419 (ttm170) cc_final: 0.8148 (ttp-110) REVERT: S 109 MET cc_start: 0.7761 (mpt) cc_final: 0.7380 (mpt) outliers start: 14 outliers final: 9 residues processed: 202 average time/residue: 0.8222 time to fit residues: 172.5252 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 : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 143 ASN Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain G residue 112 MET 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 P residue 139 MET Chi-restraints excluded: chain T residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 L 143 ASN M 108 ASN R 97 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.126087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.098560 restraints weight = 6415.018| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.28 r_work: 0.3283 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.151 7480 Z= 0.293 Angle : 1.284 59.200 10000 Z= 0.758 Chirality : 0.050 0.608 960 Planarity : 0.006 0.057 1320 Dihedral : 4.973 40.405 1040 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.43 % Allowed : 23.57 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.31 (0.18), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.14), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 136 TYR 0.005 0.001 TYR B 128 PHE 0.007 0.001 PHE E 141 TRP 0.007 0.001 TRP O 99 HIS 0.002 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 7480) covalent geometry : angle 1.28351 (10000) hydrogen bonds : bond 0.02596 ( 97) hydrogen bonds : angle 4.53525 ( 288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3353.30 seconds wall clock time: 57 minutes 52.63 seconds (3472.63 seconds total)