Starting phenix.real_space_refine on Tue May 7 08:15:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzx_37963/05_2024/8wzx_37963.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzx_37963/05_2024/8wzx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzx_37963/05_2024/8wzx_37963.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzx_37963/05_2024/8wzx_37963.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzx_37963/05_2024/8wzx_37963.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzx_37963/05_2024/8wzx_37963.pdb" } 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 Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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: 4.20, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 2.49 Conformation dependent library (CDL) restraints added in 1.3 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: 1.20 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 100 removed outlier: 6.595A pdb=" N ASN A 97 " --> pdb=" O GLN C 98 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASN C 100 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N TRP A 99 " --> pdb=" O ASN C 100 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN C 97 " --> pdb=" O GLN E 98 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ASN E 100 " --> pdb=" O ASN C 97 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TRP C 99 " --> pdb=" O ASN E 100 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASN E 97 " --> pdb=" O GLN G 98 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN G 100 " --> pdb=" O ASN E 97 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N TRP E 99 " --> pdb=" O ASN G 100 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN G 97 " --> pdb=" O GLN I 98 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ASN I 100 " --> pdb=" O ASN G 97 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N TRP G 99 " --> pdb=" O ASN I 100 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN I 97 " --> pdb=" O GLN K 98 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ASN K 100 " --> pdb=" O ASN I 97 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TRP I 99 " --> pdb=" O ASN K 100 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASN K 97 " --> pdb=" O GLN M 98 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ASN M 100 " --> pdb=" O ASN K 97 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TRP K 99 " --> pdb=" O ASN M 100 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN M 97 " --> pdb=" O GLN O 98 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASN O 100 " --> pdb=" O ASN M 97 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TRP M 99 " --> pdb=" O ASN O 100 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN O 97 " --> pdb=" O GLN Q 98 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN Q 100 " --> pdb=" O ASN O 97 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TRP O 99 " --> pdb=" O ASN Q 100 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN Q 97 " --> pdb=" O GLN S 98 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN S 100 " --> pdb=" O ASN Q 97 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TRP Q 99 " --> pdb=" O ASN S 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 110 removed outlier: 6.591A pdb=" N LYS A 106 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N MET C 109 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASN A 108 " --> pdb=" O MET C 109 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS C 106 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N MET E 109 " --> pdb=" O LYS C 106 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASN C 108 " --> pdb=" O MET E 109 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS E 106 " --> pdb=" O THR G 107 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N MET G 109 " --> pdb=" O LYS E 106 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASN E 108 " --> pdb=" O MET G 109 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS G 106 " --> pdb=" O THR I 107 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N MET I 109 " --> pdb=" O LYS G 106 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASN G 108 " --> pdb=" O MET I 109 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS I 106 " --> pdb=" O THR K 107 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N MET K 109 " --> pdb=" O LYS I 106 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASN I 108 " --> pdb=" O MET K 109 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS K 106 " --> pdb=" O THR M 107 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N MET M 109 " --> pdb=" O LYS K 106 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASN K 108 " --> pdb=" O MET M 109 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS M 106 " --> pdb=" O THR O 107 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N MET O 109 " --> pdb=" O LYS M 106 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASN M 108 " --> pdb=" O MET O 109 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS O 106 " --> pdb=" O THR Q 107 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N MET Q 109 " --> pdb=" O LYS O 106 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASN O 108 " --> pdb=" O MET Q 109 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS Q 106 " --> pdb=" O THR S 107 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N MET S 109 " --> pdb=" O LYS Q 106 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASN Q 108 " --> pdb=" O MET S 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 118 removed outlier: 6.819A pdb=" N GLY A 114 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY C 114 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY E 114 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY G 114 " --> pdb=" O ALA I 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 123 Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.185A pdb=" N ALA A 133 " --> pdb=" O MET C 134 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA C 133 " --> pdb=" O MET E 134 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA E 133 " --> pdb=" O MET G 134 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA G 133 " --> pdb=" O MET I 134 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA I 133 " --> pdb=" O MET K 134 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA K 133 " --> pdb=" O MET M 134 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA M 133 " --> pdb=" O MET O 134 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA O 133 " --> pdb=" O MET Q 134 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ALA Q 133 " --> pdb=" O MET S 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 138 through 140 removed outlier: 6.298A pdb=" N MET A 139 " --> pdb=" O HIS C 140 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N MET C 139 " --> pdb=" O HIS E 140 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N MET E 139 " --> pdb=" O HIS G 140 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N MET G 139 " --> pdb=" O HIS I 140 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N MET I 139 " --> pdb=" O HIS K 140 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N MET K 139 " --> pdb=" O HIS M 140 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N MET M 139 " --> pdb=" O HIS O 140 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N MET O 139 " --> pdb=" O HIS Q 140 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N MET Q 139 " --> pdb=" O HIS S 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 96 through 100 removed outlier: 6.585A pdb=" N ASN B 97 " --> pdb=" O GLN D 98 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ASN D 100 " --> pdb=" O ASN B 97 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N TRP B 99 " --> pdb=" O ASN D 100 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN D 97 " --> pdb=" O GLN F 98 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ASN F 100 " --> pdb=" O ASN D 97 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N TRP D 99 " --> pdb=" O ASN F 100 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN F 97 " --> pdb=" O GLN H 98 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASN H 100 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TRP F 99 " --> pdb=" O ASN H 100 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN H 97 " --> pdb=" O GLN J 98 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN J 100 " --> pdb=" O ASN H 97 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TRP H 99 " --> pdb=" O ASN J 100 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN J 97 " --> pdb=" O GLN L 98 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ASN L 100 " --> pdb=" O ASN J 97 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TRP J 99 " --> pdb=" O ASN L 100 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN L 97 " --> pdb=" O GLN N 98 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ASN N 100 " --> pdb=" O ASN L 97 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N TRP L 99 " --> pdb=" O ASN N 100 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN N 97 " --> pdb=" O GLN P 98 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ASN P 100 " --> pdb=" O ASN N 97 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TRP N 99 " --> pdb=" O ASN P 100 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN P 97 " --> pdb=" O GLN R 98 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ASN R 100 " --> pdb=" O ASN P 97 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TRP P 99 " --> pdb=" O ASN R 100 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN R 97 " --> pdb=" O GLN T 98 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ASN T 100 " --> pdb=" O ASN R 97 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TRP R 99 " --> pdb=" O ASN T 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 106 through 110 removed outlier: 6.598A pdb=" N LYS B 106 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N MET D 109 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASN B 108 " --> pdb=" O MET D 109 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS D 106 " --> pdb=" O THR F 107 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N MET F 109 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASN D 108 " --> pdb=" O MET F 109 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS F 106 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N MET H 109 " --> pdb=" O LYS F 106 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASN F 108 " --> pdb=" O MET H 109 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS H 106 " --> pdb=" O THR J 107 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N MET J 109 " --> pdb=" O LYS H 106 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASN H 108 " --> pdb=" O MET J 109 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS J 106 " --> pdb=" O THR L 107 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N MET L 109 " --> pdb=" O LYS J 106 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ASN J 108 " --> pdb=" O MET L 109 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS L 106 " --> pdb=" O THR N 107 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N MET N 109 " --> pdb=" O LYS L 106 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASN L 108 " --> pdb=" O MET N 109 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LYS N 106 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N MET P 109 " --> pdb=" O LYS N 106 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASN N 108 " --> pdb=" O MET P 109 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS P 106 " --> pdb=" O THR R 107 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N MET R 109 " --> pdb=" O LYS P 106 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASN P 108 " --> pdb=" O MET R 109 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS R 106 " --> pdb=" O THR T 107 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N MET T 109 " --> pdb=" O LYS R 106 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASN R 108 " --> pdb=" O MET T 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.824A pdb=" N GLY F 114 " --> pdb=" O ALA H 113 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 121 through 123 Processing sheet with id=AB3, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'B' and resid 133 through 135 removed outlier: 6.198A pdb=" N ALA B 133 " --> pdb=" O MET D 134 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA D 133 " --> pdb=" O MET F 134 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA F 133 " --> pdb=" O MET H 134 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA H 133 " --> pdb=" O MET J 134 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA J 133 " --> pdb=" O MET L 134 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA L 133 " --> pdb=" O MET N 134 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ALA N 133 " --> pdb=" O MET P 134 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA P 133 " --> pdb=" O MET R 134 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ALA R 133 " --> pdb=" O MET T 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 138 through 140 removed outlier: 6.311A pdb=" N MET B 139 " --> pdb=" O HIS D 140 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N MET D 139 " --> pdb=" O HIS F 140 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N MET F 139 " --> pdb=" O HIS H 140 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N MET H 139 " --> pdb=" O HIS J 140 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N MET J 139 " --> pdb=" O HIS L 140 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N MET L 139 " --> pdb=" O HIS N 140 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N MET N 139 " --> pdb=" O HIS P 140 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N MET P 139 " --> pdb=" O HIS R 140 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N MET R 139 " --> pdb=" O HIS T 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 121 through 123 Processing sheet with id=AB7, first strand: chain 'N' and resid 121 through 123 97 hydrogen bonds defined for protein. 288 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 2.73 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: 99.21 - 106.18: 333 106.18 - 113.14: 4025 113.14 - 120.11: 2050 120.11 - 127.07: 3432 127.07 - 134.03: 160 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 2.520 nonbonded pdb=" ND1 HIS P 111 " pdb=" O PHE P 141 " model vdw 2.604 2.520 nonbonded pdb=" ND1 HIS N 111 " pdb=" O PHE N 141 " model vdw 2.605 2.520 nonbonded pdb=" ND1 HIS G 111 " pdb=" O PHE G 141 " model vdw 2.605 2.520 nonbonded pdb=" ND1 HIS B 111 " pdb=" O PHE B 141 " model vdw 2.605 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 5.170 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.670 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.610 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 0.714 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: 1.6447 time to fit residues: 330.2030 Evaluate side-chains 188 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 186 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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: 2.9990 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7480 Z= 0.201 Angle : 0.649 5.909 10000 Z= 0.296 Chirality : 0.040 0.165 960 Planarity : 0.004 0.028 1320 Dihedral : 4.533 13.713 1045 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.14 % Allowed : 14.57 % 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: -4.19 (0.17), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (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 0.007 0.002 PHE L 141 TYR 0.004 0.001 TYR Q 128 ARG 0.006 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 215 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 193 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8327 (mtpp) cc_final: 0.7914 (mptt) REVERT: B 101 LYS cc_start: 0.8650 (mtpp) cc_final: 0.8066 (mttt) REVERT: C 101 LYS cc_start: 0.8526 (mtpp) cc_final: 0.7977 (mttt) REVERT: D 138 MET cc_start: 0.7513 (mtp) cc_final: 0.7246 (mtt) REVERT: E 106 LYS cc_start: 0.8001 (ptpt) cc_final: 0.7520 (ptmm) REVERT: E 138 MET cc_start: 0.7567 (mtp) cc_final: 0.7348 (mtm) REVERT: G 106 LYS cc_start: 0.7994 (ptpt) cc_final: 0.7475 (ptmm) REVERT: G 138 MET cc_start: 0.7340 (mtp) cc_final: 0.6939 (mtt) REVERT: H 106 LYS cc_start: 0.7745 (ptpt) cc_final: 0.7388 (ptmm) REVERT: I 106 LYS cc_start: 0.7984 (ptpt) cc_final: 0.7248 (ptmt) REVERT: P 109 MET cc_start: 0.7458 (mtm) cc_final: 0.7076 (mtm) REVERT: Q 138 MET cc_start: 0.7474 (mtp) cc_final: 0.7041 (mtt) REVERT: R 136 ARG cc_start: 0.7664 (ttm170) cc_final: 0.7458 (mtm180) outliers start: 22 outliers final: 0 residues processed: 196 average time/residue: 1.6345 time to fit residues: 333.2226 Evaluate side-chains 190 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 0.0770 chunk 98 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- 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 M 98 GLN N 143 ASN O 97 ASN O 143 ASN P 97 ASN R 97 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 7480 Z= 0.430 Angle : 0.693 5.674 10000 Z= 0.332 Chirality : 0.043 0.135 960 Planarity : 0.004 0.038 1320 Dihedral : 4.937 14.762 1040 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.14 % Allowed : 18.00 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.007 0.001 TRP D 99 HIS 0.005 0.001 HIS B 96 PHE 0.011 0.003 PHE K 141 TYR 0.006 0.002 TYR P 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 225 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 196 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8373 (mtpp) cc_final: 0.7930 (mptt) REVERT: A 129 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7238 (tpp) REVERT: B 101 LYS cc_start: 0.8708 (mtpp) cc_final: 0.8040 (mptt) REVERT: C 101 LYS cc_start: 0.8573 (mtpp) cc_final: 0.8008 (mttt) REVERT: E 106 LYS cc_start: 0.8009 (ptpt) cc_final: 0.7537 (ptmm) REVERT: E 138 MET cc_start: 0.7625 (mtp) cc_final: 0.7355 (mtt) REVERT: G 106 LYS cc_start: 0.8056 (ptpt) cc_final: 0.7488 (ptmm) REVERT: G 138 MET cc_start: 0.7475 (mtp) cc_final: 0.7059 (mtt) REVERT: H 106 LYS cc_start: 0.7868 (ptpt) cc_final: 0.7365 (ptmm) REVERT: I 106 LYS cc_start: 0.8087 (ptpt) cc_final: 0.7226 (ptmt) REVERT: N 101 LYS cc_start: 0.8265 (mtpp) cc_final: 0.7988 (ttmp) REVERT: N 138 MET cc_start: 0.7404 (mtp) cc_final: 0.7166 (mtt) REVERT: P 109 MET cc_start: 0.7440 (mtm) cc_final: 0.7067 (mtm) REVERT: Q 138 MET cc_start: 0.7515 (mtp) cc_final: 0.7104 (mtt) REVERT: S 109 MET cc_start: 0.7523 (mpp) cc_final: 0.7215 (mpt) REVERT: T 109 MET cc_start: 0.7247 (mpt) cc_final: 0.6822 (mpt) REVERT: T 136 ARG cc_start: 0.8049 (ttp-110) cc_final: 0.7659 (ttp-110) outliers start: 29 outliers final: 9 residues processed: 199 average time/residue: 1.6570 time to fit residues: 342.8830 Evaluate side-chains 205 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 195 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain I residue 139 MET Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain L residue 95 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 80 optimal weight: 0.0030 chunk 54 optimal weight: 0.6980 overall best weight: 2.1396 ------------------------------------------------------------------------------- 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 I 143 ASN N 97 ASN N 143 ASN O 143 ASN R 97 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 7480 Z= 0.386 Angle : 0.671 5.685 10000 Z= 0.321 Chirality : 0.043 0.137 960 Planarity : 0.004 0.041 1320 Dihedral : 4.866 14.115 1040 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 5.29 % Allowed : 17.71 % Favored : 77.00 % 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: -4.21 (0.17), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.13), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 99 HIS 0.004 0.001 HIS B 96 PHE 0.011 0.002 PHE G 141 TYR 0.006 0.002 TYR B 128 ARG 0.007 0.001 ARG H 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 234 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 197 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8376 (mtpp) cc_final: 0.7866 (mptt) REVERT: A 129 MET cc_start: 0.7462 (ttp) cc_final: 0.7232 (tpp) REVERT: B 101 LYS cc_start: 0.8718 (mtpp) cc_final: 0.8068 (mptt) REVERT: C 101 LYS cc_start: 0.8577 (mtpp) cc_final: 0.8021 (mttt) REVERT: D 138 MET cc_start: 0.7583 (mtp) cc_final: 0.7230 (mtt) REVERT: E 106 LYS cc_start: 0.8005 (ptpt) cc_final: 0.7533 (ptmm) REVERT: E 138 MET cc_start: 0.7643 (mtp) cc_final: 0.7382 (mtt) REVERT: G 106 LYS cc_start: 0.8033 (ptpt) cc_final: 0.7463 (ptmm) REVERT: G 138 MET cc_start: 0.7492 (mtp) cc_final: 0.7084 (mtt) REVERT: H 106 LYS cc_start: 0.8002 (ptpt) cc_final: 0.7388 (ptmm) REVERT: I 106 LYS cc_start: 0.8079 (ptpt) cc_final: 0.7188 (ptmt) REVERT: I 136 ARG cc_start: 0.7879 (ttm110) cc_final: 0.7652 (ttp-110) REVERT: N 138 MET cc_start: 0.7412 (mtp) cc_final: 0.7174 (mtt) REVERT: P 109 MET cc_start: 0.7426 (mtm) cc_final: 0.7125 (mtm) REVERT: Q 138 MET cc_start: 0.7520 (mtp) cc_final: 0.7117 (mtt) REVERT: S 109 MET cc_start: 0.7499 (mpp) cc_final: 0.7176 (mpt) REVERT: S 138 MET cc_start: 0.7792 (mtp) cc_final: 0.7570 (mtt) REVERT: T 109 MET cc_start: 0.7210 (mpt) cc_final: 0.6478 (mpt) outliers start: 37 outliers final: 8 residues processed: 207 average time/residue: 1.6069 time to fit residues: 346.3077 Evaluate side-chains 202 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 194 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain G residue 143 ASN 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 L residue 112 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 L 143 ASN N 143 ASN O 143 ASN R 97 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 7480 Z= 0.511 Angle : 0.738 5.864 10000 Z= 0.355 Chirality : 0.045 0.174 960 Planarity : 0.005 0.047 1320 Dihedral : 5.118 15.877 1040 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 5.71 % Allowed : 18.00 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.16), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.12), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 99 HIS 0.005 0.001 HIS B 96 PHE 0.011 0.003 PHE N 141 TYR 0.008 0.002 TYR P 128 ARG 0.007 0.001 ARG H 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 230 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 190 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8407 (mtpp) cc_final: 0.7891 (mptt) REVERT: A 129 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7240 (tpp) REVERT: B 101 LYS cc_start: 0.8729 (mtpp) cc_final: 0.8068 (mptt) REVERT: C 101 LYS cc_start: 0.8588 (mtpp) cc_final: 0.8038 (mttt) REVERT: C 134 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.7148 (mtm) REVERT: D 138 MET cc_start: 0.7551 (mtp) cc_final: 0.7198 (mtt) REVERT: E 106 LYS cc_start: 0.8007 (ptpt) cc_final: 0.7516 (ptmm) REVERT: E 138 MET cc_start: 0.7667 (mtp) cc_final: 0.7384 (mtt) REVERT: G 106 LYS cc_start: 0.8090 (ptpt) cc_final: 0.7455 (ptmm) REVERT: G 112 MET cc_start: 0.7692 (ptp) cc_final: 0.7045 (mtm) REVERT: G 138 MET cc_start: 0.7541 (mtp) cc_final: 0.7158 (mtt) REVERT: H 106 LYS cc_start: 0.8024 (ptpt) cc_final: 0.7353 (ptmm) REVERT: I 106 LYS cc_start: 0.8126 (ptpt) cc_final: 0.7318 (ptmt) REVERT: N 138 MET cc_start: 0.7424 (mtp) cc_final: 0.7181 (mtt) REVERT: P 109 MET cc_start: 0.7446 (mtm) cc_final: 0.7064 (mtm) REVERT: Q 138 MET cc_start: 0.7596 (mtp) cc_final: 0.7206 (mtt) REVERT: R 136 ARG cc_start: 0.8129 (mtp180) cc_final: 0.7754 (mtp180) REVERT: S 109 MET cc_start: 0.7485 (mpp) cc_final: 0.7179 (mpt) REVERT: S 138 MET cc_start: 0.7826 (mtp) cc_final: 0.7560 (mtt) REVERT: T 109 MET cc_start: 0.7305 (mpt) cc_final: 0.6478 (mpt) outliers start: 40 outliers final: 13 residues processed: 200 average time/residue: 1.6918 time to fit residues: 351.8323 Evaluate side-chains 205 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 190 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 139 MET Chi-restraints excluded: chain I residue 139 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 T residue 134 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 96 optimal weight: 0.0170 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- 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 I 143 ASN N 143 ASN R 97 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7480 Z= 0.242 Angle : 0.642 7.938 10000 Z= 0.297 Chirality : 0.041 0.185 960 Planarity : 0.004 0.041 1320 Dihedral : 4.587 13.105 1040 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.43 % Allowed : 20.43 % 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 (0.17), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.13), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 99 HIS 0.002 0.001 HIS B 96 PHE 0.008 0.001 PHE G 141 TYR 0.004 0.001 TYR B 128 ARG 0.009 0.001 ARG H 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 225 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 194 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8357 (mtpp) cc_final: 0.7845 (mptt) REVERT: A 129 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7283 (tpp) REVERT: B 101 LYS cc_start: 0.8678 (mtpp) cc_final: 0.8058 (mttt) REVERT: C 101 LYS cc_start: 0.8589 (mtpp) cc_final: 0.8032 (mttt) REVERT: C 138 MET cc_start: 0.7634 (mtp) cc_final: 0.7395 (mtp) REVERT: D 138 MET cc_start: 0.7516 (mtp) cc_final: 0.7153 (mtt) REVERT: E 106 LYS cc_start: 0.8030 (ptpt) cc_final: 0.7511 (ptmm) REVERT: E 138 MET cc_start: 0.7608 (mtp) cc_final: 0.7336 (mtt) REVERT: G 106 LYS cc_start: 0.8052 (ptpt) cc_final: 0.7432 (ptmm) REVERT: G 138 MET cc_start: 0.7474 (mtp) cc_final: 0.7067 (mtt) REVERT: H 106 LYS cc_start: 0.7985 (ptpt) cc_final: 0.7378 (ptmm) REVERT: H 109 MET cc_start: 0.7228 (mtm) cc_final: 0.7027 (mtm) REVERT: H 138 MET cc_start: 0.7531 (mtp) cc_final: 0.7208 (mtt) REVERT: I 106 LYS cc_start: 0.8131 (ptpt) cc_final: 0.7245 (ptmt) REVERT: M 112 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7293 (ptp) REVERT: N 138 MET cc_start: 0.7350 (mtp) cc_final: 0.7105 (mtt) REVERT: P 109 MET cc_start: 0.7379 (mtm) cc_final: 0.7002 (mtm) REVERT: Q 138 MET cc_start: 0.7507 (mtp) cc_final: 0.7121 (mtt) REVERT: S 109 MET cc_start: 0.7490 (mpp) cc_final: 0.7259 (mpt) REVERT: S 138 MET cc_start: 0.7732 (mtp) cc_final: 0.7517 (mtt) outliers start: 31 outliers final: 8 residues processed: 204 average time/residue: 1.6180 time to fit residues: 343.5424 Evaluate side-chains 201 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 191 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain I residue 139 MET Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain L residue 112 MET Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain T residue 134 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 0.0370 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- 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 N 97 ASN N 143 ASN R 97 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7480 Z= 0.203 Angle : 0.644 9.181 10000 Z= 0.293 Chirality : 0.042 0.196 960 Planarity : 0.004 0.048 1320 Dihedral : 4.388 13.181 1040 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.14 % Allowed : 21.00 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.18), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.14), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 99 HIS 0.002 0.000 HIS B 96 PHE 0.004 0.001 PHE J 141 TYR 0.003 0.001 TYR B 128 ARG 0.012 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 220 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 198 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8318 (mtpp) cc_final: 0.7842 (mptt) REVERT: A 106 LYS cc_start: 0.8303 (ptpt) cc_final: 0.7743 (ptmm) REVERT: A 129 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7330 (tpp) REVERT: B 101 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8006 (mttt) REVERT: C 101 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8034 (mttt) REVERT: C 138 MET cc_start: 0.7619 (mtp) cc_final: 0.7385 (mtp) REVERT: D 138 MET cc_start: 0.7538 (mtp) cc_final: 0.7194 (mtt) REVERT: E 101 LYS cc_start: 0.8684 (mtpp) cc_final: 0.8044 (mttp) REVERT: E 106 LYS cc_start: 0.8020 (ptpt) cc_final: 0.7495 (ptmm) REVERT: E 138 MET cc_start: 0.7619 (mtp) cc_final: 0.7350 (mtt) REVERT: G 106 LYS cc_start: 0.8042 (ptpt) cc_final: 0.7445 (ptmm) REVERT: G 112 MET cc_start: 0.7628 (ptp) cc_final: 0.7047 (mtm) REVERT: G 138 MET cc_start: 0.7468 (mtp) cc_final: 0.7071 (mtt) REVERT: H 106 LYS cc_start: 0.8013 (ptpt) cc_final: 0.7390 (ptmm) REVERT: H 112 MET cc_start: 0.7732 (ptp) cc_final: 0.7195 (mtp) REVERT: H 136 ARG cc_start: 0.8073 (mtp-110) cc_final: 0.7745 (mtm110) REVERT: H 138 MET cc_start: 0.7527 (mtp) cc_final: 0.7266 (mtt) REVERT: I 106 LYS cc_start: 0.8048 (ptpt) cc_final: 0.7201 (ptmt) REVERT: L 134 MET cc_start: 0.7788 (ptp) cc_final: 0.7487 (pmm) REVERT: M 112 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7321 (ptp) REVERT: N 138 MET cc_start: 0.7339 (mtp) cc_final: 0.7096 (mtt) REVERT: Q 138 MET cc_start: 0.7514 (mtp) cc_final: 0.7116 (mtt) REVERT: S 109 MET cc_start: 0.7471 (mpp) cc_final: 0.7252 (mpt) REVERT: S 138 MET cc_start: 0.7745 (mtp) cc_final: 0.7526 (mtt) outliers start: 22 outliers final: 8 residues processed: 205 average time/residue: 1.6722 time to fit residues: 356.6237 Evaluate side-chains 205 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 195 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 I residue 139 MET Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain K residue 138 MET Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain T residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 61 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 0.3980 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 I 143 ASN N 143 ASN O 97 ASN R 97 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7480 Z= 0.176 Angle : 0.647 10.466 10000 Z= 0.289 Chirality : 0.042 0.209 960 Planarity : 0.004 0.051 1320 Dihedral : 4.168 13.213 1040 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.86 % Allowed : 21.43 % Favored : 75.71 % 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: -4.11 (0.18), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.14), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 99 HIS 0.001 0.000 HIS M 111 PHE 0.004 0.001 PHE J 141 TYR 0.004 0.001 TYR M 128 ARG 0.012 0.001 ARG O 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 203 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8266 (mtpp) cc_final: 0.7824 (mptt) REVERT: A 106 LYS cc_start: 0.8292 (ptpt) cc_final: 0.7754 (ptmm) REVERT: A 129 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7341 (tpp) REVERT: B 101 LYS cc_start: 0.8582 (mtpp) cc_final: 0.7982 (mttt) REVERT: C 101 LYS cc_start: 0.8570 (mtpp) cc_final: 0.8016 (mttt) REVERT: C 112 MET cc_start: 0.7436 (ptm) cc_final: 0.6957 (tmm) REVERT: C 138 MET cc_start: 0.7592 (mtp) cc_final: 0.7365 (mtp) REVERT: D 138 MET cc_start: 0.7549 (mtp) cc_final: 0.7195 (mtt) REVERT: E 101 LYS cc_start: 0.8620 (mtpp) cc_final: 0.8053 (mttp) REVERT: E 106 LYS cc_start: 0.8014 (ptpt) cc_final: 0.7594 (ptmm) REVERT: E 138 MET cc_start: 0.7576 (mtp) cc_final: 0.7293 (mtt) REVERT: F 134 MET cc_start: 0.7215 (mtm) cc_final: 0.6958 (mmm) REVERT: G 106 LYS cc_start: 0.8046 (ptpt) cc_final: 0.7433 (ptmm) REVERT: G 112 MET cc_start: 0.7625 (ptp) cc_final: 0.7075 (mtm) REVERT: G 134 MET cc_start: 0.7341 (mtm) cc_final: 0.6983 (mtp) REVERT: G 138 MET cc_start: 0.7449 (mtp) cc_final: 0.7047 (mtt) REVERT: H 106 LYS cc_start: 0.7986 (ptpt) cc_final: 0.7403 (ptmm) REVERT: H 112 MET cc_start: 0.7734 (ptp) cc_final: 0.7242 (mtp) REVERT: H 136 ARG cc_start: 0.8027 (mtp-110) cc_final: 0.7708 (mtm110) REVERT: H 138 MET cc_start: 0.7511 (mtp) cc_final: 0.7259 (mtt) REVERT: L 112 MET cc_start: 0.7430 (ptp) cc_final: 0.7090 (ptp) REVERT: L 134 MET cc_start: 0.7834 (ptp) cc_final: 0.7611 (pmm) REVERT: M 95 THR cc_start: 0.8224 (t) cc_final: 0.7989 (m) REVERT: M 101 LYS cc_start: 0.8430 (mtpm) cc_final: 0.7566 (mttm) REVERT: N 138 MET cc_start: 0.7340 (mtp) cc_final: 0.7092 (mtt) REVERT: Q 138 MET cc_start: 0.7507 (mtp) cc_final: 0.7118 (mtt) REVERT: S 109 MET cc_start: 0.7468 (mpp) cc_final: 0.7267 (mpt) REVERT: T 109 MET cc_start: 0.7133 (mpt) cc_final: 0.6793 (mpt) outliers start: 20 outliers final: 6 residues processed: 209 average time/residue: 1.6127 time to fit residues: 350.8849 Evaluate side-chains 208 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 201 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain J residue 134 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 70 optimal weight: 0.0980 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 ASN E 97 ASN ** F 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN I 143 ASN N 143 ASN R 97 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7480 Z= 0.227 Angle : 0.671 10.536 10000 Z= 0.302 Chirality : 0.042 0.209 960 Planarity : 0.005 0.055 1320 Dihedral : 4.336 15.207 1040 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.00 % Allowed : 22.86 % 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: -4.15 (0.18), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.14), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 99 HIS 0.002 0.000 HIS M 111 PHE 0.005 0.001 PHE L 141 TYR 0.005 0.001 TYR G 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 215 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 201 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8329 (mtpp) cc_final: 0.7853 (mptt) REVERT: A 106 LYS cc_start: 0.8305 (ptpt) cc_final: 0.7816 (ptmm) REVERT: A 129 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7274 (tpp) REVERT: B 101 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8021 (mttt) REVERT: C 101 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8035 (mttt) REVERT: C 138 MET cc_start: 0.7637 (mtp) cc_final: 0.7400 (mtp) REVERT: D 138 MET cc_start: 0.7537 (mtp) cc_final: 0.7192 (mtt) REVERT: E 101 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8067 (mttp) REVERT: E 106 LYS cc_start: 0.8023 (ptpt) cc_final: 0.7599 (ptmm) REVERT: E 138 MET cc_start: 0.7588 (mtp) cc_final: 0.7317 (mtt) REVERT: F 136 ARG cc_start: 0.7577 (ttm-80) cc_final: 0.7318 (mtp180) REVERT: G 106 LYS cc_start: 0.8032 (ptpt) cc_final: 0.7432 (ptmm) REVERT: G 112 MET cc_start: 0.7664 (ptp) cc_final: 0.7191 (mtm) REVERT: G 134 MET cc_start: 0.7462 (mtm) cc_final: 0.7089 (mtp) REVERT: G 138 MET cc_start: 0.7454 (mtp) cc_final: 0.7066 (mtt) REVERT: H 106 LYS cc_start: 0.7985 (ptpt) cc_final: 0.7362 (ptmm) REVERT: H 112 MET cc_start: 0.7806 (ptp) cc_final: 0.7295 (mtp) REVERT: H 136 ARG cc_start: 0.8021 (mtp-110) cc_final: 0.7808 (mtm110) REVERT: H 138 MET cc_start: 0.7518 (mtp) cc_final: 0.7263 (mtt) REVERT: L 112 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.7098 (ptp) REVERT: L 134 MET cc_start: 0.7836 (ptp) cc_final: 0.7589 (pmm) REVERT: L 136 ARG cc_start: 0.7995 (ttm110) cc_final: 0.7795 (ttm110) REVERT: M 101 LYS cc_start: 0.8428 (mtpm) cc_final: 0.7567 (mttm) REVERT: N 138 MET cc_start: 0.7344 (mtp) cc_final: 0.7105 (mtt) REVERT: Q 138 MET cc_start: 0.7530 (mtp) cc_final: 0.7142 (mtt) REVERT: S 109 MET cc_start: 0.7456 (mpp) cc_final: 0.7235 (mpt) REVERT: T 109 MET cc_start: 0.7125 (mpt) cc_final: 0.6755 (mpt) outliers start: 14 outliers final: 7 residues processed: 206 average time/residue: 1.6426 time to fit residues: 351.8795 Evaluate side-chains 209 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 200 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 143 ASN Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain L residue 112 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 91 optimal weight: 0.0770 chunk 79 optimal weight: 0.0980 chunk 8 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN D 97 ASN E 97 ASN ** F 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 ASN I 143 ASN N 143 ASN R 97 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2388 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= 0.222 Angle : 0.691 10.433 10000 Z= 0.308 Chirality : 0.043 0.210 960 Planarity : 0.005 0.058 1320 Dihedral : 4.338 17.435 1040 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.71 % Allowed : 23.43 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.14 (0.18), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.14), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 99 HIS 0.002 0.000 HIS A 96 PHE 0.005 0.001 PHE L 141 TYR 0.006 0.001 TYR J 128 ARG 0.013 0.001 ARG P 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 217 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 205 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8327 (mtpp) cc_final: 0.7853 (mptt) REVERT: A 106 LYS cc_start: 0.8311 (ptpt) cc_final: 0.7776 (ptmm) REVERT: A 129 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7211 (tpp) REVERT: B 101 LYS cc_start: 0.8627 (mtpp) cc_final: 0.8019 (mttt) REVERT: C 101 LYS cc_start: 0.8601 (mtpp) cc_final: 0.8039 (mttt) REVERT: C 138 MET cc_start: 0.7659 (mtp) cc_final: 0.7417 (mtp) REVERT: D 138 MET cc_start: 0.7541 (mtp) cc_final: 0.7189 (mtt) REVERT: E 101 LYS cc_start: 0.8642 (mtpp) cc_final: 0.8065 (mttp) REVERT: E 106 LYS cc_start: 0.8018 (ptpt) cc_final: 0.7593 (ptmm) REVERT: E 138 MET cc_start: 0.7585 (mtp) cc_final: 0.7306 (mtt) REVERT: G 106 LYS cc_start: 0.8016 (ptpt) cc_final: 0.7397 (ptmm) REVERT: G 112 MET cc_start: 0.7656 (ptp) cc_final: 0.7203 (mtm) REVERT: G 134 MET cc_start: 0.7459 (mtm) cc_final: 0.7090 (mtp) REVERT: G 138 MET cc_start: 0.7487 (mtp) cc_final: 0.7125 (mtt) REVERT: H 106 LYS cc_start: 0.7982 (ptpt) cc_final: 0.7355 (ptmm) REVERT: H 112 MET cc_start: 0.7837 (ptp) cc_final: 0.7318 (mtp) REVERT: H 136 ARG cc_start: 0.8021 (mtp-110) cc_final: 0.7723 (mtm110) REVERT: H 138 MET cc_start: 0.7511 (mtp) cc_final: 0.7250 (mtt) REVERT: L 112 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.7103 (ptp) REVERT: L 134 MET cc_start: 0.7829 (ptp) cc_final: 0.7572 (pmm) REVERT: M 101 LYS cc_start: 0.8441 (mtpm) cc_final: 0.7570 (mttm) REVERT: N 95 THR cc_start: 0.8246 (p) cc_final: 0.7862 (t) REVERT: N 138 MET cc_start: 0.7342 (mtp) cc_final: 0.7100 (mtt) REVERT: Q 138 MET cc_start: 0.7528 (mtp) cc_final: 0.7147 (mtt) REVERT: S 109 MET cc_start: 0.7450 (mpp) cc_final: 0.7237 (mpt) REVERT: T 109 MET cc_start: 0.7121 (mpt) cc_final: 0.6753 (mpt) outliers start: 12 outliers final: 7 residues processed: 208 average time/residue: 1.5980 time to fit residues: 345.9365 Evaluate side-chains 212 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 203 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 143 ASN Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain L residue 112 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 HIS ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 ASN E 97 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 ASN R 97 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.126238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.098250 restraints weight = 6254.466| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.27 r_work: 0.3290 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7480 Z= 0.261 Angle : 0.708 10.085 10000 Z= 0.317 Chirality : 0.043 0.236 960 Planarity : 0.005 0.059 1320 Dihedral : 4.444 14.177 1040 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.71 % Allowed : 24.43 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.16 (0.18), residues: 980 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.14), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 99 HIS 0.002 0.001 HIS B 96 PHE 0.006 0.002 PHE F 141 TYR 0.008 0.001 TYR K 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: 4933.03 seconds wall clock time: 87 minutes 59.63 seconds (5279.63 seconds total)