Starting phenix.real_space_refine on Tue Jan 14 20:11:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wzx_37963/01_2025/8wzx_37963.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wzx_37963/01_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_37963/01_2025/8wzx_37963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wzx_37963/01_2025/8wzx_37963.map" model { file = "/net/cci-nas-00/data/ceres_data/8wzx_37963/01_2025/8wzx_37963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wzx_37963/01_2025/8wzx_37963.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 4500 2.51 5 N 1400 2.21 5 O 1280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7300 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "B" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "C" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "D" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "E" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "F" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "G" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "H" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "I" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "J" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "K" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "L" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "M" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "N" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "O" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "P" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "Q" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "R" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "S" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "T" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 365 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Time building chain proxies: 4.90, per 1000 atoms: 0.67 Number of scatterers: 7300 At special positions: 0 Unit cell: (58.93, 98.77, 71.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 1280 8.00 N 1400 7.00 C 4500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 1.1 seconds 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 100 removed outlier: 6.595A pdb=" N ASN A 97 " --> pdb=" O GLN C 98 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASN C 100 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N TRP A 99 " --> pdb=" O ASN C 100 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN C 97 " --> pdb=" O GLN E 98 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ASN E 100 " --> pdb=" O ASN C 97 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TRP C 99 " --> pdb=" O ASN E 100 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASN E 97 " --> pdb=" O GLN G 98 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN G 100 " --> pdb=" O ASN E 97 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N TRP E 99 " --> pdb=" O ASN G 100 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN G 97 " --> pdb=" O GLN I 98 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ASN I 100 " --> pdb=" O ASN G 97 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N TRP G 99 " --> pdb=" O ASN I 100 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN I 97 " --> pdb=" O GLN K 98 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ASN K 100 " --> pdb=" O ASN I 97 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TRP I 99 " --> pdb=" O ASN K 100 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASN K 97 " --> pdb=" O GLN M 98 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ASN M 100 " --> pdb=" O ASN K 97 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TRP K 99 " --> pdb=" O ASN M 100 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN M 97 " --> pdb=" O GLN O 98 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASN O 100 " --> pdb=" O ASN M 97 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TRP M 99 " --> pdb=" O ASN O 100 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN O 97 " --> pdb=" O GLN Q 98 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN Q 100 " --> pdb=" O ASN O 97 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TRP O 99 " --> pdb=" O ASN Q 100 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN Q 97 " --> pdb=" O GLN S 98 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN S 100 " --> pdb=" O ASN Q 97 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TRP Q 99 " --> pdb=" O ASN S 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 110 removed outlier: 6.591A pdb=" N LYS A 106 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N MET C 109 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASN A 108 " --> pdb=" O MET C 109 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS C 106 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N MET E 109 " --> pdb=" O LYS C 106 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASN C 108 " --> pdb=" O MET E 109 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS E 106 " --> pdb=" O THR G 107 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N MET G 109 " --> pdb=" O LYS E 106 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASN E 108 " --> pdb=" O MET G 109 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS G 106 " --> pdb=" O THR I 107 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N MET I 109 " --> pdb=" O LYS G 106 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASN G 108 " --> pdb=" O MET I 109 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS I 106 " --> pdb=" O THR K 107 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N MET K 109 " --> pdb=" O LYS I 106 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASN I 108 " --> pdb=" O MET K 109 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS K 106 " --> pdb=" O THR M 107 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N MET M 109 " --> pdb=" O LYS K 106 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASN K 108 " --> pdb=" O MET M 109 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS M 106 " --> pdb=" O THR O 107 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N MET O 109 " --> pdb=" O LYS M 106 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASN M 108 " --> pdb=" O MET O 109 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS O 106 " --> pdb=" O THR Q 107 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N MET Q 109 " --> pdb=" O LYS O 106 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASN O 108 " --> pdb=" O MET Q 109 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS Q 106 " --> pdb=" O THR S 107 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N MET S 109 " --> pdb=" O LYS Q 106 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASN Q 108 " --> pdb=" O MET S 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 118 removed outlier: 6.819A pdb=" N GLY A 114 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY C 114 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY E 114 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY G 114 " --> pdb=" O ALA I 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 123 Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.185A pdb=" N ALA A 133 " --> pdb=" O MET C 134 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA C 133 " --> pdb=" O MET E 134 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA E 133 " --> pdb=" O MET G 134 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA G 133 " --> pdb=" O MET I 134 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA I 133 " --> pdb=" O MET K 134 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA K 133 " --> pdb=" O MET M 134 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA M 133 " --> pdb=" O MET O 134 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA O 133 " --> pdb=" O MET Q 134 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ALA Q 133 " --> pdb=" O MET S 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 138 through 140 removed outlier: 6.298A pdb=" N MET A 139 " --> pdb=" O HIS C 140 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N MET C 139 " --> pdb=" O HIS E 140 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N MET E 139 " --> pdb=" O HIS G 140 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N MET G 139 " --> pdb=" O HIS I 140 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N MET I 139 " --> pdb=" O HIS K 140 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N MET K 139 " --> pdb=" O HIS M 140 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N MET M 139 " --> pdb=" O HIS O 140 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N MET O 139 " --> pdb=" O HIS Q 140 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N MET Q 139 " --> pdb=" O HIS S 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 96 through 100 removed outlier: 6.585A pdb=" N ASN B 97 " --> pdb=" O GLN D 98 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ASN D 100 " --> pdb=" O ASN B 97 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N TRP B 99 " --> pdb=" O ASN D 100 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN D 97 " --> pdb=" O GLN F 98 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ASN F 100 " --> pdb=" O ASN D 97 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N TRP D 99 " --> pdb=" O ASN F 100 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN F 97 " --> pdb=" O GLN H 98 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASN H 100 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TRP F 99 " --> pdb=" O ASN H 100 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN H 97 " --> pdb=" O GLN J 98 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN J 100 " --> pdb=" O ASN H 97 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TRP H 99 " --> pdb=" O ASN J 100 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN J 97 " --> pdb=" O GLN L 98 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ASN L 100 " --> pdb=" O ASN J 97 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TRP J 99 " --> pdb=" O ASN L 100 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN L 97 " --> pdb=" O GLN N 98 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ASN N 100 " --> pdb=" O ASN L 97 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N TRP L 99 " --> pdb=" O ASN N 100 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN N 97 " --> pdb=" O GLN P 98 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ASN P 100 " --> pdb=" O ASN N 97 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TRP N 99 " --> pdb=" O ASN P 100 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN P 97 " --> pdb=" O GLN R 98 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ASN R 100 " --> pdb=" O ASN P 97 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TRP P 99 " --> pdb=" O ASN R 100 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN R 97 " --> pdb=" O GLN T 98 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ASN T 100 " --> pdb=" O ASN R 97 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TRP R 99 " --> pdb=" O ASN T 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 106 through 110 removed outlier: 6.598A pdb=" N LYS B 106 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N MET D 109 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASN B 108 " --> pdb=" O MET D 109 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS D 106 " --> pdb=" O THR F 107 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N MET F 109 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASN D 108 " --> pdb=" O MET F 109 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS F 106 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N MET H 109 " --> pdb=" O LYS F 106 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASN F 108 " --> pdb=" O MET H 109 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS H 106 " --> pdb=" O THR J 107 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N MET J 109 " --> pdb=" O LYS H 106 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASN H 108 " --> pdb=" O MET J 109 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS J 106 " --> pdb=" O THR L 107 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N MET L 109 " --> pdb=" O LYS J 106 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ASN J 108 " --> pdb=" O MET L 109 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS L 106 " --> pdb=" O THR N 107 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N MET N 109 " --> pdb=" O LYS L 106 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASN L 108 " --> pdb=" O MET N 109 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LYS N 106 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N MET P 109 " --> pdb=" O LYS N 106 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASN N 108 " --> pdb=" O MET P 109 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS P 106 " --> pdb=" O THR R 107 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N MET R 109 " --> pdb=" O LYS P 106 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASN P 108 " --> pdb=" O MET R 109 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS R 106 " --> pdb=" O THR T 107 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N MET T 109 " --> pdb=" O LYS R 106 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASN R 108 " --> pdb=" O MET T 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.824A pdb=" N GLY F 114 " --> pdb=" O ALA H 113 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 121 through 123 Processing sheet with id=AB3, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'B' and resid 133 through 135 removed outlier: 6.198A pdb=" N ALA B 133 " --> pdb=" O MET D 134 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA D 133 " --> pdb=" O MET F 134 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA F 133 " --> pdb=" O MET H 134 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA H 133 " --> pdb=" O MET J 134 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA J 133 " --> pdb=" O MET L 134 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA L 133 " --> pdb=" O MET N 134 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ALA N 133 " --> pdb=" O MET P 134 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA P 133 " --> pdb=" O MET R 134 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ALA R 133 " --> pdb=" O MET T 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 138 through 140 removed outlier: 6.311A pdb=" N MET B 139 " --> pdb=" O HIS D 140 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N MET D 139 " --> pdb=" O HIS F 140 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N MET F 139 " --> pdb=" O HIS H 140 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N MET H 139 " --> pdb=" O HIS J 140 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N MET J 139 " --> pdb=" O HIS L 140 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N MET L 139 " --> pdb=" O HIS N 140 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N MET N 139 " --> pdb=" O HIS P 140 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N MET P 139 " --> pdb=" O HIS R 140 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N MET R 139 " --> pdb=" O HIS T 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 121 through 123 Processing sheet with id=AB7, first strand: chain 'N' and resid 121 through 123 97 hydrogen bonds defined for protein. 288 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 2.16 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.550 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.047 7480 Z= 0.655 Angle : 0.972 7.748 10000 Z= 0.461 Chirality : 0.057 0.178 960 Planarity : 0.005 0.019 1320 Dihedral : 10.359 44.003 2700 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.17), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.13), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP Q 99 HIS 0.006 0.002 HIS R 96 PHE 0.018 0.005 PHE R 141 TYR 0.005 0.003 TYR H 128 ARG 0.001 0.000 ARG K 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8308 (mtpp) cc_final: 0.7907 (mptt) REVERT: B 101 LYS cc_start: 0.8615 (mtpp) cc_final: 0.7999 (mptt) REVERT: C 138 MET cc_start: 0.7655 (mtp) cc_final: 0.7442 (mtp) REVERT: D 138 MET cc_start: 0.7576 (mtp) cc_final: 0.7318 (mtt) REVERT: E 106 LYS cc_start: 0.8011 (ptpt) cc_final: 0.7408 (ptmm) REVERT: E 138 MET cc_start: 0.7618 (mtp) cc_final: 0.7342 (mtt) REVERT: F 136 ARG cc_start: 0.7605 (ttm170) cc_final: 0.7402 (ttp-170) REVERT: G 106 LYS cc_start: 0.8038 (ptpt) cc_final: 0.7487 (ptmm) REVERT: G 138 MET cc_start: 0.7457 (mtp) cc_final: 0.7069 (mtt) REVERT: H 106 LYS cc_start: 0.7777 (ptpt) cc_final: 0.7296 (ptmm) REVERT: I 106 LYS cc_start: 0.8049 (ptpt) cc_final: 0.7323 (ptmt) REVERT: O 138 MET cc_start: 0.7447 (mtp) cc_final: 0.7245 (mtp) REVERT: Q 138 MET cc_start: 0.7566 (mtp) cc_final: 0.7318 (mtt) REVERT: R 136 ARG cc_start: 0.7723 (ttm170) cc_final: 0.7499 (mtp-110) REVERT: S 138 MET cc_start: 0.7719 (mtp) cc_final: 0.7416 (mtt) outliers start: 0 outliers final: 2 residues processed: 193 average time/residue: 1.6727 time to fit residues: 335.4801 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 : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 134 MET Chi-restraints excluded: chain H residue 143 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 ASN C 143 ASN D 97 ASN D 143 ASN E 97 ASN E 143 ASN F 143 ASN G 143 ASN I 143 ASN L 100 ASN N 143 ASN O 98 GLN O 143 ASN P 143 ASN Q 97 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.126480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.099274 restraints weight = 6469.542| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.31 r_work: 0.3270 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 7480 Z= 0.201 Angle : 0.655 5.962 10000 Z= 0.300 Chirality : 0.041 0.164 960 Planarity : 0.004 0.027 1320 Dihedral : 4.583 13.925 1045 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.29 % Allowed : 14.43 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.17), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.13), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 99 HIS 0.003 0.001 HIS B 96 PHE 0.006 0.001 PHE L 141 TYR 0.003 0.001 TYR Q 128 ARG 0.007 0.001 ARG O 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 195 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7564 (mptt) REVERT: B 101 LYS cc_start: 0.8530 (mtpp) cc_final: 0.7812 (mttt) REVERT: C 101 LYS cc_start: 0.8303 (mtpp) cc_final: 0.7639 (mttt) REVERT: C 134 MET cc_start: 0.8445 (ptp) cc_final: 0.8165 (pmm) REVERT: D 138 MET cc_start: 0.8584 (mtp) cc_final: 0.8282 (mtt) REVERT: D 143 ASN cc_start: 0.8807 (m-40) cc_final: 0.8525 (m-40) REVERT: E 106 LYS cc_start: 0.7595 (ptpt) cc_final: 0.7086 (ptmm) REVERT: E 138 MET cc_start: 0.8645 (mtp) cc_final: 0.8415 (mtm) REVERT: F 136 ARG cc_start: 0.8242 (ttm170) cc_final: 0.7984 (ttm-80) REVERT: F 143 ASN cc_start: 0.9103 (OUTLIER) cc_final: 0.8835 (m110) REVERT: G 106 LYS cc_start: 0.7631 (ptpt) cc_final: 0.7028 (ptmm) REVERT: G 138 MET cc_start: 0.8368 (mtp) cc_final: 0.7883 (mtt) REVERT: H 106 LYS cc_start: 0.7523 (ptpt) cc_final: 0.7146 (ptmm) REVERT: I 106 LYS cc_start: 0.7627 (ptpt) cc_final: 0.6767 (ptmt) REVERT: M 129 MET cc_start: 0.8620 (ttp) cc_final: 0.8384 (ttt) REVERT: P 109 MET cc_start: 0.8095 (mtm) cc_final: 0.7690 (mtm) REVERT: Q 138 MET cc_start: 0.8511 (mtp) cc_final: 0.8003 (mtt) REVERT: R 136 ARG cc_start: 0.8415 (ttm170) cc_final: 0.8052 (mtm180) REVERT: S 109 MET cc_start: 0.7880 (mpt) cc_final: 0.7612 (mpt) REVERT: T 136 ARG cc_start: 0.8598 (ttp-110) cc_final: 0.8380 (ttp-110) outliers start: 23 outliers final: 0 residues processed: 198 average time/residue: 1.6215 time to fit residues: 333.9751 Evaluate side-chains 191 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 143 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 54 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 4 optimal weight: 0.2980 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.125389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.098045 restraints weight = 6460.700| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.29 r_work: 0.3256 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 7480 Z= 0.314 Angle : 0.652 5.323 10000 Z= 0.309 Chirality : 0.042 0.136 960 Planarity : 0.004 0.033 1320 Dihedral : 4.707 14.569 1040 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.43 % Allowed : 16.86 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.17), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.13), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 99 HIS 0.004 0.001 HIS B 96 PHE 0.009 0.002 PHE K 141 TYR 0.005 0.001 TYR B 128 ARG 0.007 0.001 ARG O 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8257 (mtpp) cc_final: 0.7579 (mptt) REVERT: A 129 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7508 (tpp) REVERT: B 101 LYS cc_start: 0.8565 (mtpp) cc_final: 0.7835 (mttt) REVERT: C 101 LYS cc_start: 0.8359 (mtpp) cc_final: 0.7687 (mttt) REVERT: D 138 MET cc_start: 0.8660 (mtp) cc_final: 0.8369 (mtt) REVERT: E 106 LYS cc_start: 0.7700 (ptpt) cc_final: 0.7202 (ptmm) REVERT: E 138 MET cc_start: 0.8704 (mtp) cc_final: 0.8425 (mtt) REVERT: E 143 ASN cc_start: 0.8847 (m-40) cc_final: 0.8622 (m-40) REVERT: F 136 ARG cc_start: 0.8315 (ttm170) cc_final: 0.8045 (ttm-80) REVERT: G 106 LYS cc_start: 0.7706 (ptpt) cc_final: 0.7064 (ptmm) REVERT: G 134 MET cc_start: 0.8600 (ptp) cc_final: 0.8217 (mtm) REVERT: G 138 MET cc_start: 0.8468 (mtp) cc_final: 0.8024 (mtt) REVERT: H 106 LYS cc_start: 0.7658 (ptpt) cc_final: 0.7137 (ptmm) REVERT: I 106 LYS cc_start: 0.7749 (ptpt) cc_final: 0.6888 (ptmt) REVERT: I 136 ARG cc_start: 0.8530 (ttm110) cc_final: 0.8231 (ttp-110) REVERT: M 101 LYS cc_start: 0.8476 (mtpm) cc_final: 0.7471 (mttm) REVERT: M 129 MET cc_start: 0.8644 (ttp) cc_final: 0.8426 (ttt) REVERT: N 138 MET cc_start: 0.8420 (mtp) cc_final: 0.8121 (mtt) REVERT: P 109 MET cc_start: 0.8066 (mtm) cc_final: 0.7677 (mtm) REVERT: Q 138 MET cc_start: 0.8587 (mtp) cc_final: 0.8129 (mtt) REVERT: R 136 ARG cc_start: 0.8381 (ttm170) cc_final: 0.8127 (mtp-110) REVERT: S 109 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7715 (mpt) REVERT: T 109 MET cc_start: 0.7920 (mpt) cc_final: 0.7654 (mpt) outliers start: 31 outliers final: 8 residues processed: 203 average time/residue: 1.6413 time to fit residues: 346.5423 Evaluate side-chains 206 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 196 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 L residue 95 THR Chi-restraints excluded: chain N residue 112 MET Chi-restraints excluded: chain O residue 112 MET Chi-restraints excluded: chain S residue 109 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 3 optimal weight: 0.0570 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN D 97 ASN D 143 ASN E 97 ASN G 143 ASN I 143 ASN J 143 ASN N 143 ASN O 98 GLN O 143 ASN P 97 ASN R 97 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.125156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.097750 restraints weight = 6399.156| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.28 r_work: 0.3250 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 7480 Z= 0.329 Angle : 0.652 6.030 10000 Z= 0.309 Chirality : 0.042 0.166 960 Planarity : 0.004 0.037 1320 Dihedral : 4.740 14.014 1040 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.71 % Allowed : 16.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.17), 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 TRP 0.006 0.001 TRP C 99 HIS 0.004 0.001 HIS B 96 PHE 0.008 0.002 PHE L 141 TYR 0.008 0.002 TYR L 128 ARG 0.008 0.001 ARG O 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8262 (mtpp) cc_final: 0.7545 (mptt) REVERT: A 129 MET cc_start: 0.7903 (ttp) cc_final: 0.7665 (tpp) REVERT: A 136 ARG cc_start: 0.8672 (ttm-80) cc_final: 0.8368 (ttm-80) REVERT: B 101 LYS cc_start: 0.8565 (mtpp) cc_final: 0.7798 (mttt) REVERT: C 101 LYS cc_start: 0.8341 (mtpp) cc_final: 0.7652 (mttt) REVERT: D 138 MET cc_start: 0.8617 (mtp) cc_final: 0.8311 (mtt) REVERT: D 143 ASN cc_start: 0.8676 (m-40) cc_final: 0.8421 (m110) REVERT: E 106 LYS cc_start: 0.7651 (ptpt) cc_final: 0.7111 (ptmm) REVERT: E 138 MET cc_start: 0.8647 (mtp) cc_final: 0.8374 (mtt) REVERT: F 134 MET cc_start: 0.8536 (ptp) cc_final: 0.8246 (mtm) REVERT: G 106 LYS cc_start: 0.7656 (ptpt) cc_final: 0.6997 (ptmm) REVERT: G 138 MET cc_start: 0.8397 (mtp) cc_final: 0.7943 (mtt) REVERT: H 106 LYS cc_start: 0.7710 (ptpt) cc_final: 0.7098 (ptmm) REVERT: I 106 LYS cc_start: 0.7688 (ptpt) cc_final: 0.6843 (ptmt) REVERT: I 134 MET cc_start: 0.8540 (ptp) cc_final: 0.8284 (mtm) REVERT: M 129 MET cc_start: 0.8621 (ttp) cc_final: 0.8387 (ttt) REVERT: N 138 MET cc_start: 0.8427 (mtp) cc_final: 0.8125 (mtt) REVERT: P 109 MET cc_start: 0.8082 (mtm) cc_final: 0.7757 (mtm) REVERT: Q 138 MET cc_start: 0.8544 (mtp) cc_final: 0.8086 (mtt) REVERT: R 136 ARG cc_start: 0.8423 (ttm170) cc_final: 0.8122 (mtp-110) REVERT: S 109 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7640 (mpt) REVERT: S 138 MET cc_start: 0.8650 (mtp) cc_final: 0.8418 (mtt) outliers start: 40 outliers final: 7 residues processed: 209 average time/residue: 1.5921 time to fit residues: 346.2223 Evaluate side-chains 202 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 194 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain K residue 138 MET Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain N residue 112 MET Chi-restraints excluded: chain O residue 112 MET Chi-restraints excluded: chain S residue 109 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 0.0060 overall best weight: 1.5600 ------------------------------------------------------------------------------- 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 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 = 0.3818 r_free = 0.3818 target = 0.125271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.097842 restraints weight = 6369.787| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.28 r_work: 0.3266 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7480 Z= 0.297 Angle : 0.663 6.879 10000 Z= 0.308 Chirality : 0.042 0.169 960 Planarity : 0.004 0.041 1320 Dihedral : 4.679 14.605 1040 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.57 % Allowed : 19.86 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.17), 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 TRP 0.006 0.001 TRP D 99 HIS 0.003 0.001 HIS B 96 PHE 0.007 0.002 PHE K 141 TYR 0.005 0.001 TYR B 128 ARG 0.009 0.001 ARG O 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8258 (mtpp) cc_final: 0.7535 (mptt) REVERT: A 129 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7676 (tpp) REVERT: B 101 LYS cc_start: 0.8557 (mtpp) cc_final: 0.7813 (mttt) REVERT: C 101 LYS cc_start: 0.8391 (mtpp) cc_final: 0.7694 (mttt) REVERT: C 136 ARG cc_start: 0.8536 (ttp-110) cc_final: 0.8228 (ttm-80) REVERT: D 138 MET cc_start: 0.8611 (mtp) cc_final: 0.8302 (mtt) REVERT: D 143 ASN cc_start: 0.8605 (m-40) cc_final: 0.8364 (m110) REVERT: E 101 LYS cc_start: 0.8551 (mtpp) cc_final: 0.7792 (mttp) REVERT: E 106 LYS cc_start: 0.7663 (ptpt) cc_final: 0.7114 (ptmm) REVERT: E 138 MET cc_start: 0.8619 (mtp) cc_final: 0.8343 (mtt) REVERT: F 134 MET cc_start: 0.8498 (ptp) cc_final: 0.8236 (mtm) REVERT: G 106 LYS cc_start: 0.7716 (ptpt) cc_final: 0.7013 (ptmm) REVERT: G 112 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7574 (mtm) REVERT: G 138 MET cc_start: 0.8425 (mtp) cc_final: 0.7974 (mtt) REVERT: H 106 LYS cc_start: 0.7728 (ptpt) cc_final: 0.7105 (ptmm) REVERT: H 138 MET cc_start: 0.8471 (mtp) cc_final: 0.8100 (mtt) REVERT: I 106 LYS cc_start: 0.7758 (ptpt) cc_final: 0.6784 (ptmt) REVERT: I 134 MET cc_start: 0.8558 (ptp) cc_final: 0.8207 (mtm) REVERT: M 129 MET cc_start: 0.8604 (ttp) cc_final: 0.8400 (ttt) REVERT: N 138 MET cc_start: 0.8401 (mtp) cc_final: 0.8103 (mtt) REVERT: Q 138 MET cc_start: 0.8559 (mtp) cc_final: 0.8119 (mtt) REVERT: R 136 ARG cc_start: 0.8432 (ttm170) cc_final: 0.8169 (mtp-110) REVERT: S 109 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7718 (mpt) REVERT: S 138 MET cc_start: 0.8651 (mtp) cc_final: 0.8424 (mtt) outliers start: 32 outliers final: 10 residues processed: 210 average time/residue: 1.6277 time to fit residues: 355.3205 Evaluate side-chains 212 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 G residue 112 MET Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L 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 134 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 8 optimal weight: 0.0010 chunk 86 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN D 97 ASN E 97 ASN E 143 ASN J 143 ASN L 143 ASN 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 = 0.3858 r_free = 0.3858 target = 0.127665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.100339 restraints weight = 6252.294| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.27 r_work: 0.3297 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2148 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= 0.182 Angle : 0.629 8.370 10000 Z= 0.285 Chirality : 0.041 0.169 960 Planarity : 0.004 0.045 1320 Dihedral : 4.330 15.566 1040 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.71 % Allowed : 21.14 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.18), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.14), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 99 HIS 0.002 0.000 HIS A 111 PHE 0.004 0.001 PHE K 141 TYR 0.004 0.001 TYR B 128 ARG 0.010 0.001 ARG P 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7564 (mptt) REVERT: A 106 LYS cc_start: 0.8037 (ptpt) cc_final: 0.7442 (ptmm) REVERT: A 129 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7702 (tpp) REVERT: B 101 LYS cc_start: 0.8478 (mtpp) cc_final: 0.7745 (mttt) REVERT: C 136 ARG cc_start: 0.8472 (ttp-110) cc_final: 0.8158 (ttm-80) REVERT: D 138 MET cc_start: 0.8601 (mtp) cc_final: 0.8292 (mtt) REVERT: E 101 LYS cc_start: 0.8561 (mtpp) cc_final: 0.7816 (mttp) REVERT: E 106 LYS cc_start: 0.7647 (ptpt) cc_final: 0.7095 (ptmm) REVERT: E 138 MET cc_start: 0.8600 (mtp) cc_final: 0.8367 (mtt) REVERT: F 97 ASN cc_start: 0.9077 (m-40) cc_final: 0.8873 (m110) REVERT: G 106 LYS cc_start: 0.7685 (ptpt) cc_final: 0.7009 (ptmm) REVERT: G 112 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7450 (mtm) REVERT: G 134 MET cc_start: 0.8481 (ptp) cc_final: 0.8258 (mtm) REVERT: G 138 MET cc_start: 0.8358 (mtp) cc_final: 0.7904 (mtt) REVERT: H 106 LYS cc_start: 0.7701 (ptpt) cc_final: 0.7135 (ptmm) REVERT: H 136 ARG cc_start: 0.8601 (mtp-110) cc_final: 0.8281 (mtm110) REVERT: H 138 MET cc_start: 0.8450 (mtp) cc_final: 0.8093 (mtt) REVERT: I 134 MET cc_start: 0.8529 (ptp) cc_final: 0.8209 (mtm) REVERT: K 112 MET cc_start: 0.8259 (ptp) cc_final: 0.7930 (mtm) REVERT: N 138 MET cc_start: 0.8370 (mtp) cc_final: 0.8069 (mtt) REVERT: P 138 MET cc_start: 0.8440 (mtt) cc_final: 0.8153 (mmm) REVERT: Q 138 MET cc_start: 0.8504 (mtp) cc_final: 0.8032 (mtt) REVERT: R 136 ARG cc_start: 0.8350 (ttm170) cc_final: 0.8063 (mtp-110) outliers start: 26 outliers final: 6 residues processed: 214 average time/residue: 1.5841 time to fit residues: 352.8422 Evaluate side-chains 209 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 201 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 G residue 112 MET Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain P residue 112 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 3 optimal weight: 0.0050 chunk 87 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- 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 J 143 ASN L 143 ASN M 98 GLN O 143 ASN P 98 GLN R 97 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.124667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.096778 restraints weight = 6396.964| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.30 r_work: 0.3239 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2093 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= 0.395 Angle : 0.709 7.331 10000 Z= 0.332 Chirality : 0.045 0.190 960 Planarity : 0.005 0.049 1320 Dihedral : 4.826 14.798 1040 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.71 % Allowed : 21.57 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.17), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.13), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 99 HIS 0.005 0.001 HIS C 96 PHE 0.009 0.002 PHE L 141 TYR 0.007 0.002 TYR B 128 ARG 0.011 0.001 ARG O 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 0.834 Fit side-chains REVERT: A 101 LYS cc_start: 0.8293 (mtpp) cc_final: 0.7555 (mptt) REVERT: A 129 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7673 (tpp) REVERT: B 101 LYS cc_start: 0.8588 (mtpp) cc_final: 0.7842 (mttt) REVERT: C 101 LYS cc_start: 0.8415 (mtpp) cc_final: 0.7665 (mttt) REVERT: E 101 LYS cc_start: 0.8574 (mtpp) cc_final: 0.7800 (mttp) REVERT: E 106 LYS cc_start: 0.7668 (ptpt) cc_final: 0.7102 (ptmm) REVERT: E 138 MET cc_start: 0.8661 (mtp) cc_final: 0.8388 (mtt) REVERT: G 106 LYS cc_start: 0.7682 (ptpt) cc_final: 0.7019 (ptmm) REVERT: G 112 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7720 (mtm) REVERT: G 136 ARG cc_start: 0.8382 (ttm170) cc_final: 0.7919 (mtm110) REVERT: G 138 MET cc_start: 0.8429 (mtp) cc_final: 0.7993 (mtt) REVERT: H 104 LYS cc_start: 0.8149 (mttt) cc_final: 0.7631 (mtpp) REVERT: H 106 LYS cc_start: 0.7755 (ptpt) cc_final: 0.7042 (ptmm) REVERT: H 112 MET cc_start: 0.8558 (ptp) cc_final: 0.7909 (mtp) REVERT: I 134 MET cc_start: 0.8567 (ptp) cc_final: 0.8187 (mtm) REVERT: J 109 MET cc_start: 0.7972 (mtm) cc_final: 0.7640 (mtm) REVERT: J 112 MET cc_start: 0.8389 (ptp) cc_final: 0.7916 (mtm) REVERT: K 112 MET cc_start: 0.8295 (ptp) cc_final: 0.7945 (mtm) REVERT: N 138 MET cc_start: 0.8436 (mtp) cc_final: 0.8149 (mtt) REVERT: Q 138 MET cc_start: 0.8596 (mtp) cc_final: 0.8156 (mtt) REVERT: R 136 ARG cc_start: 0.8431 (ttm170) cc_final: 0.8165 (mtp-110) REVERT: S 109 MET cc_start: 0.7777 (mpt) cc_final: 0.7380 (mpt) REVERT: S 138 MET cc_start: 0.8693 (mtp) cc_final: 0.8436 (mtt) outliers start: 26 outliers final: 12 residues processed: 209 average time/residue: 1.6564 time to fit residues: 360.0463 Evaluate side-chains 214 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 H 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 110 LYS Chi-restraints excluded: chain P residue 112 MET Chi-restraints excluded: chain P residue 139 MET Chi-restraints excluded: chain T residue 134 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN D 97 ASN E 97 ASN E 143 ASN J 100 ASN J 143 ASN L 143 ASN O 143 ASN R 97 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.127363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.099617 restraints weight = 6321.747| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.29 r_work: 0.3281 rms_B_bonded: 2.30 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: 0.8520 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7480 Z= 0.205 Angle : 0.676 9.705 10000 Z= 0.302 Chirality : 0.043 0.205 960 Planarity : 0.004 0.052 1320 Dihedral : 4.416 14.854 1040 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.86 % Allowed : 21.86 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.18), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.14), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 99 HIS 0.002 0.000 HIS A 111 PHE 0.005 0.001 PHE I 141 TYR 0.004 0.001 TYR B 128 ARG 0.013 0.001 ARG H 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8243 (mtpp) cc_final: 0.7558 (mptt) REVERT: A 106 LYS cc_start: 0.8054 (ptpt) cc_final: 0.7390 (ptmm) REVERT: A 129 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7618 (tpp) REVERT: B 101 LYS cc_start: 0.8537 (mtpp) cc_final: 0.7801 (mttt) REVERT: C 136 ARG cc_start: 0.8423 (ttp-110) cc_final: 0.8052 (ttm-80) REVERT: E 101 LYS cc_start: 0.8579 (mtpp) cc_final: 0.7831 (mttp) REVERT: E 106 LYS cc_start: 0.7609 (ptpt) cc_final: 0.7159 (ptmm) REVERT: E 138 MET cc_start: 0.8621 (mtp) cc_final: 0.8395 (mtm) REVERT: G 106 LYS cc_start: 0.7668 (ptpt) cc_final: 0.6994 (ptmm) REVERT: G 112 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7628 (mtm) REVERT: G 134 MET cc_start: 0.8471 (ptp) cc_final: 0.8251 (mtm) REVERT: G 138 MET cc_start: 0.8366 (mtp) cc_final: 0.7925 (mtt) REVERT: H 106 LYS cc_start: 0.7800 (ptpt) cc_final: 0.7129 (ptmm) REVERT: H 112 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7786 (mtm) REVERT: H 136 ARG cc_start: 0.8602 (mtp-110) cc_final: 0.8138 (mtm110) REVERT: H 138 MET cc_start: 0.8465 (mtp) cc_final: 0.8124 (mtt) REVERT: I 134 MET cc_start: 0.8510 (ptp) cc_final: 0.8203 (mtm) REVERT: J 109 MET cc_start: 0.7975 (mtm) cc_final: 0.7598 (mtm) REVERT: K 112 MET cc_start: 0.8325 (ptp) cc_final: 0.7965 (mtm) REVERT: L 95 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7791 (m) REVERT: L 134 MET cc_start: 0.8650 (ptp) cc_final: 0.8368 (pmm) REVERT: N 138 MET cc_start: 0.8381 (mtp) cc_final: 0.8079 (mtt) REVERT: Q 138 MET cc_start: 0.8526 (mtp) cc_final: 0.8078 (mtt) REVERT: R 136 ARG cc_start: 0.8385 (ttm170) cc_final: 0.8101 (ttp-110) outliers start: 27 outliers final: 8 residues processed: 212 average time/residue: 1.6681 time to fit residues: 367.7374 Evaluate side-chains 212 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 H residue 112 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 134 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 25 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 91 optimal weight: 0.0020 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 ASN E 97 ASN E 143 ASN J 143 ASN L 143 ASN M 98 GLN O 143 ASN P 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 = 0.3862 r_free = 0.3862 target = 0.127508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.099439 restraints weight = 6346.409| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.30 r_work: 0.3288 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7480 Z= 0.213 Angle : 0.684 9.124 10000 Z= 0.307 Chirality : 0.043 0.216 960 Planarity : 0.005 0.054 1320 Dihedral : 4.424 19.132 1040 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.14 % Allowed : 22.57 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.18), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.14), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 99 HIS 0.002 0.000 HIS A 111 PHE 0.005 0.001 PHE G 141 TYR 0.004 0.001 TYR B 128 ARG 0.013 0.001 ARG O 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8245 (mtpp) cc_final: 0.7555 (mptt) REVERT: A 106 LYS cc_start: 0.8064 (ptpt) cc_final: 0.7409 (ptmm) REVERT: A 129 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7660 (tpp) REVERT: B 101 LYS cc_start: 0.8512 (mtpp) cc_final: 0.7785 (mttt) REVERT: C 101 LYS cc_start: 0.8381 (mtpp) cc_final: 0.7664 (mttt) REVERT: E 101 LYS cc_start: 0.8568 (mtpp) cc_final: 0.7809 (mttp) REVERT: E 106 LYS cc_start: 0.7637 (ptpt) cc_final: 0.7184 (ptmm) REVERT: E 138 MET cc_start: 0.8605 (mtp) cc_final: 0.8370 (mtm) REVERT: G 106 LYS cc_start: 0.7644 (ptpt) cc_final: 0.6838 (ptmm) REVERT: G 112 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7695 (mtm) REVERT: G 134 MET cc_start: 0.8467 (ptp) cc_final: 0.8229 (mtm) REVERT: G 138 MET cc_start: 0.8391 (mtp) cc_final: 0.7928 (mtt) REVERT: H 106 LYS cc_start: 0.7830 (ptpt) cc_final: 0.7152 (ptmm) REVERT: H 112 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7819 (mtm) REVERT: H 136 ARG cc_start: 0.8595 (mtp-110) cc_final: 0.8118 (mtm110) REVERT: H 138 MET cc_start: 0.8455 (mtp) cc_final: 0.8129 (mtt) REVERT: I 134 MET cc_start: 0.8513 (ptp) cc_final: 0.8201 (mtm) REVERT: J 109 MET cc_start: 0.7980 (mtm) cc_final: 0.7613 (mtm) REVERT: K 112 MET cc_start: 0.8348 (ptp) cc_final: 0.8014 (mtm) REVERT: L 112 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7864 (ttm) REVERT: L 134 MET cc_start: 0.8635 (ptp) cc_final: 0.8402 (pmm) REVERT: M 112 MET cc_start: 0.8425 (ptp) cc_final: 0.8176 (ptp) REVERT: M 134 MET cc_start: 0.8649 (ptp) cc_final: 0.8443 (mtm) REVERT: N 138 MET cc_start: 0.8386 (mtp) cc_final: 0.8088 (mtt) REVERT: P 138 MET cc_start: 0.8552 (mtt) cc_final: 0.8236 (mmm) REVERT: Q 138 MET cc_start: 0.8518 (mtp) cc_final: 0.8071 (mtt) REVERT: R 136 ARG cc_start: 0.8370 (ttm170) cc_final: 0.8079 (ttp-110) outliers start: 22 outliers final: 9 residues processed: 210 average time/residue: 1.6907 time to fit residues: 368.9308 Evaluate side-chains 215 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 H residue 112 MET Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 112 MET Chi-restraints excluded: chain P residue 139 MET Chi-restraints excluded: chain T residue 134 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 97 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN D 97 ASN E 97 ASN E 143 ASN F 143 ASN H 97 ASN J 143 ASN L 143 ASN O 143 ASN R 97 ASN R 100 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.123272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.095421 restraints weight = 6515.885| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.29 r_work: 0.3229 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 7480 Z= 0.517 Angle : 0.801 8.967 10000 Z= 0.375 Chirality : 0.049 0.286 960 Planarity : 0.005 0.057 1320 Dihedral : 5.035 16.201 1040 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.86 % Allowed : 23.00 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.34 (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 TRP 0.006 0.001 TRP C 99 HIS 0.006 0.001 HIS B 96 PHE 0.013 0.003 PHE C 141 TYR 0.009 0.002 TYR B 128 ARG 0.012 0.001 ARG O 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 0.876 Fit side-chains REVERT: A 101 LYS cc_start: 0.8349 (mtpp) cc_final: 0.7600 (mptt) REVERT: A 129 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7685 (tpp) REVERT: A 136 ARG cc_start: 0.8668 (ttm-80) cc_final: 0.8420 (ttm-80) REVERT: B 101 LYS cc_start: 0.8628 (mtpp) cc_final: 0.7835 (mptt) REVERT: B 136 ARG cc_start: 0.8759 (ttm-80) cc_final: 0.8551 (ttm110) REVERT: E 106 LYS cc_start: 0.7704 (ptpt) cc_final: 0.7125 (ptmm) REVERT: E 138 MET cc_start: 0.8662 (mtp) cc_final: 0.8388 (mtt) REVERT: G 106 LYS cc_start: 0.7711 (ptpt) cc_final: 0.7022 (ptmm) REVERT: G 112 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7794 (mtm) REVERT: G 136 ARG cc_start: 0.8330 (ttm170) cc_final: 0.7931 (mtm110) REVERT: G 138 MET cc_start: 0.8490 (mtp) cc_final: 0.8059 (mtt) REVERT: H 104 LYS cc_start: 0.8166 (mttt) cc_final: 0.7647 (mtpp) REVERT: H 106 LYS cc_start: 0.7739 (ptpt) cc_final: 0.7022 (ptmm) REVERT: H 112 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8030 (mtm) REVERT: H 138 MET cc_start: 0.8479 (mtp) cc_final: 0.8123 (mtt) REVERT: I 134 MET cc_start: 0.8588 (ptp) cc_final: 0.8196 (mtm) REVERT: J 109 MET cc_start: 0.8004 (mtm) cc_final: 0.7635 (mtm) REVERT: J 112 MET cc_start: 0.8456 (ptp) cc_final: 0.7988 (mtm) REVERT: K 112 MET cc_start: 0.8386 (ptp) cc_final: 0.8033 (mtm) REVERT: L 112 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7906 (mtm) REVERT: N 138 MET cc_start: 0.8400 (mtp) cc_final: 0.8118 (mtt) REVERT: Q 138 MET cc_start: 0.8617 (mtp) cc_final: 0.8192 (mtt) REVERT: R 136 ARG cc_start: 0.8438 (ttm170) cc_final: 0.8152 (mtp-110) REVERT: S 109 MET cc_start: 0.8185 (mpp) cc_final: 0.7925 (mpt) REVERT: S 138 MET cc_start: 0.8635 (mtp) cc_final: 0.8366 (mtt) outliers start: 20 outliers final: 10 residues processed: 204 average time/residue: 1.7002 time to fit residues: 360.4360 Evaluate side-chains 214 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain G residue 112 MET Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 112 MET Chi-restraints excluded: chain P residue 139 MET Chi-restraints excluded: chain T residue 134 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 96 optimal weight: 0.0670 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- 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 J 143 ASN L 143 ASN M 98 GLN O 143 ASN R 97 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.123786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.096177 restraints weight = 6349.458| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.26 r_work: 0.3242 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 7480 Z= 0.384 Angle : 1.101 59.199 10000 Z= 0.597 Chirality : 0.051 0.751 960 Planarity : 0.005 0.055 1320 Dihedral : 5.230 45.179 1040 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.16 % Favored : 96.73 % Rotamer: Outliers : 2.43 % Allowed : 24.57 % Favored : 73.00 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (0.17), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.13), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 99 HIS 0.005 0.001 HIS B 96 PHE 0.010 0.003 PHE C 141 TYR 0.007 0.002 TYR B 128 ARG 0.013 0.001 ARG O 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6610.27 seconds wall clock time: 117 minutes 39.46 seconds (7059.46 seconds total)