Starting phenix.real_space_refine on Mon Apr 8 01:54:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6teb_10479/04_2024/6teb_10479.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6teb_10479/04_2024/6teb_10479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6teb_10479/04_2024/6teb_10479.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6teb_10479/04_2024/6teb_10479.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6teb_10479/04_2024/6teb_10479.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6teb_10479/04_2024/6teb_10479.pdb" } resolution = 4.14 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 12 5.16 5 C 7662 2.51 5 N 2166 2.21 5 O 2328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ARG 31": "NH1" <-> "NH2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 170": "NH1" <-> "NH2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "E ARG 31": "NH1" <-> "NH2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 80": "NH1" <-> "NH2" Residue "E PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F ARG 31": "NH1" <-> "NH2" Residue "F ARG 51": "NH1" <-> "NH2" Residue "F ARG 60": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G ARG 44": "NH1" <-> "NH2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "G PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 44": "NH1" <-> "NH2" Residue "H ARG 69": "NH1" <-> "NH2" Residue "H ARG 170": "NH1" <-> "NH2" Residue "H PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 28": "NH1" <-> "NH2" Residue "I ARG 31": "NH1" <-> "NH2" Residue "I ARG 51": "NH1" <-> "NH2" Residue "I ARG 60": "NH1" <-> "NH2" Residue "I ARG 80": "NH1" <-> "NH2" Residue "I PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 28": "NH1" <-> "NH2" Residue "J ARG 31": "NH1" <-> "NH2" Residue "J ARG 51": "NH1" <-> "NH2" Residue "J ARG 60": "NH1" <-> "NH2" Residue "J ARG 80": "NH1" <-> "NH2" Residue "J PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 21": "OE1" <-> "OE2" Residue "K ARG 44": "NH1" <-> "NH2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K ARG 170": "NH1" <-> "NH2" Residue "K PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 44": "NH1" <-> "NH2" Residue "L ARG 69": "NH1" <-> "NH2" Residue "L ARG 170": "NH1" <-> "NH2" Residue "L PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12168 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "B" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "D" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1056 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1056 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "F" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "G" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1056 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1056 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "J" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "K" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1056 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1056 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 6.42, per 1000 atoms: 0.53 Number of scatterers: 12168 At special positions: 0 Unit cell: (106.3, 106.3, 90.355, 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 12 16.00 O 2328 8.00 N 2166 7.00 C 7662 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: 4.67 Conformation dependent library (CDL) restraints added in 2.2 seconds 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2832 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 21 sheets defined 10.2% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA B 79 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 3.576A pdb=" N VAL D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA D 64 " --> pdb=" O GLU D 60 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE D 65 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 3.570A pdb=" N VAL C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA C 64 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA E 79 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG E 80 " --> pdb=" O ASP E 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG F 80 " --> pdb=" O ASP F 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 3.575A pdb=" N VAL G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA G 64 " --> pdb=" O GLU G 60 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE G 65 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 68 removed outlier: 3.571A pdb=" N VAL H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG H 61 " --> pdb=" O ASP H 57 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE H 65 " --> pdb=" O ARG H 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA I 79 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG I 80 " --> pdb=" O ASP I 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA J 79 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG J 80 " --> pdb=" O ASP J 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 68 removed outlier: 3.576A pdb=" N VAL K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG K 61 " --> pdb=" O ASP K 57 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA K 64 " --> pdb=" O GLU K 60 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE K 65 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 68 removed outlier: 3.570A pdb=" N VAL L 59 " --> pdb=" O SER L 55 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG L 61 " --> pdb=" O ASP L 57 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA L 64 " --> pdb=" O GLU L 60 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE L 65 " --> pdb=" O ARG L 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE L 66 " --> pdb=" O LEU L 62 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 22 through 23 removed outlier: 5.685A pdb=" N ILE A 107 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA A 127 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA A 62 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 22 through 23 removed outlier: 6.077A pdb=" N THR A 108 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A 110 " --> pdb=" O PHE B 34 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA B 62 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA B 127 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ILE B 107 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 25 through 26 removed outlier: 3.609A pdb=" N GLU D 25 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN D 37 " --> pdb=" O GLU D 25 " (cutoff:3.500A) No H-bonds generated for sheet with id= 3 Processing sheet with id= 4, first strand: chain 'D' and resid 52 through 54 removed outlier: 3.942A pdb=" N GLY D 52 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU D 200 " --> pdb=" O GLY D 52 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG D 54 " --> pdb=" O GLY D 198 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 158 through 159 Processing sheet with id= 6, first strand: chain 'C' and resid 52 through 54 removed outlier: 3.944A pdb=" N GLY C 52 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU C 200 " --> pdb=" O GLY C 52 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG C 54 " --> pdb=" O GLY C 198 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA C 197 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 158 through 159 Processing sheet with id= 8, first strand: chain 'E' and resid 22 through 23 removed outlier: 5.686A pdb=" N ILE E 107 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA E 127 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA E 62 " --> pdb=" O SER E 128 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'E' and resid 22 through 23 removed outlier: 6.077A pdb=" N THR E 108 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE E 110 " --> pdb=" O PHE F 34 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA F 62 " --> pdb=" O SER F 128 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA F 127 " --> pdb=" O ILE F 107 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ILE F 107 " --> pdb=" O ALA F 127 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'G' and resid 25 through 26 removed outlier: 3.609A pdb=" N GLU G 25 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN G 37 " --> pdb=" O GLU G 25 " (cutoff:3.500A) No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'G' and resid 52 through 54 removed outlier: 3.942A pdb=" N GLY G 52 " --> pdb=" O LEU G 200 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU G 200 " --> pdb=" O GLY G 52 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG G 54 " --> pdb=" O GLY G 198 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA G 197 " --> pdb=" O GLN G 193 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'G' and resid 158 through 159 Processing sheet with id= 13, first strand: chain 'H' and resid 52 through 54 removed outlier: 3.944A pdb=" N GLY H 52 " --> pdb=" O LEU H 200 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU H 200 " --> pdb=" O GLY H 52 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG H 54 " --> pdb=" O GLY H 198 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA H 197 " --> pdb=" O GLN H 193 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'H' and resid 158 through 159 Processing sheet with id= 15, first strand: chain 'I' and resid 22 through 23 removed outlier: 5.685A pdb=" N ILE I 107 " --> pdb=" O ALA I 127 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA I 127 " --> pdb=" O ILE I 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA I 62 " --> pdb=" O SER I 128 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'I' and resid 22 through 23 removed outlier: 6.076A pdb=" N THR I 108 " --> pdb=" O ALA J 36 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE I 110 " --> pdb=" O PHE J 34 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ALA J 62 " --> pdb=" O SER J 128 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA J 127 " --> pdb=" O ILE J 107 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ILE J 107 " --> pdb=" O ALA J 127 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'K' and resid 25 through 26 removed outlier: 3.609A pdb=" N GLU K 25 " --> pdb=" O ASN K 37 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN K 37 " --> pdb=" O GLU K 25 " (cutoff:3.500A) No H-bonds generated for sheet with id= 17 Processing sheet with id= 18, first strand: chain 'K' and resid 52 through 54 removed outlier: 3.943A pdb=" N GLY K 52 " --> pdb=" O LEU K 200 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU K 200 " --> pdb=" O GLY K 52 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG K 54 " --> pdb=" O GLY K 198 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA K 197 " --> pdb=" O GLN K 193 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'K' and resid 158 through 159 Processing sheet with id= 20, first strand: chain 'L' and resid 52 through 54 removed outlier: 3.944A pdb=" N GLY L 52 " --> pdb=" O LEU L 200 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU L 200 " --> pdb=" O GLY L 52 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG L 54 " --> pdb=" O GLY L 198 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA L 197 " --> pdb=" O GLN L 193 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'L' and resid 158 through 159 303 hydrogen bonds defined for protein. 801 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: 3.36 Time building geometry restraints manager: 4.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4166 1.34 - 1.45: 1982 1.45 - 1.57: 6260 1.57 - 1.68: 0 1.68 - 1.80: 24 Bond restraints: 12432 Sorted by residual: bond pdb=" N THR L 185 " pdb=" CA THR L 185 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.21e-02 6.83e+03 8.69e+00 bond pdb=" N THR C 185 " pdb=" CA THR C 185 " ideal model delta sigma weight residual 1.455 1.491 -0.035 1.21e-02 6.83e+03 8.58e+00 bond pdb=" N THR H 185 " pdb=" CA THR H 185 " ideal model delta sigma weight residual 1.455 1.491 -0.035 1.21e-02 6.83e+03 8.52e+00 bond pdb=" N VAL L 192 " pdb=" CA VAL L 192 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.24e-02 6.50e+03 8.09e+00 bond pdb=" N THR G 185 " pdb=" CA THR G 185 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.21e-02 6.83e+03 8.08e+00 ... (remaining 12427 not shown) Histogram of bond angle deviations from ideal: 101.18 - 107.75: 669 107.75 - 114.32: 6516 114.32 - 120.90: 5473 120.90 - 127.47: 4046 127.47 - 134.04: 120 Bond angle restraints: 16824 Sorted by residual: angle pdb=" C ILE F 107 " pdb=" N THR F 108 " pdb=" CA THR F 108 " ideal model delta sigma weight residual 121.54 130.18 -8.64 1.91e+00 2.74e-01 2.05e+01 angle pdb=" C ILE I 107 " pdb=" N THR I 108 " pdb=" CA THR I 108 " ideal model delta sigma weight residual 121.54 130.18 -8.64 1.91e+00 2.74e-01 2.04e+01 angle pdb=" C ILE A 107 " pdb=" N THR A 108 " pdb=" CA THR A 108 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.04e+01 angle pdb=" C ILE J 107 " pdb=" N THR J 108 " pdb=" CA THR J 108 " ideal model delta sigma weight residual 121.54 130.15 -8.61 1.91e+00 2.74e-01 2.03e+01 angle pdb=" C ILE B 107 " pdb=" N THR B 108 " pdb=" CA THR B 108 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 ... (remaining 16819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.47: 6423 15.47 - 30.95: 645 30.95 - 46.42: 159 46.42 - 61.90: 9 61.90 - 77.37: 18 Dihedral angle restraints: 7254 sinusoidal: 2844 harmonic: 4410 Sorted by residual: dihedral pdb=" CA GLN D 72 " pdb=" C GLN D 72 " pdb=" N LEU D 73 " pdb=" CA LEU D 73 " ideal model delta harmonic sigma weight residual -180.00 -151.96 -28.04 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA GLN K 72 " pdb=" C GLN K 72 " pdb=" N LEU K 73 " pdb=" CA LEU K 73 " ideal model delta harmonic sigma weight residual -180.00 -151.96 -28.04 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA GLN G 72 " pdb=" C GLN G 72 " pdb=" N LEU G 73 " pdb=" CA LEU G 73 " ideal model delta harmonic sigma weight residual -180.00 -151.96 -28.04 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 7251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1519 0.091 - 0.182: 248 0.182 - 0.273: 21 0.273 - 0.364: 0 0.364 - 0.455: 12 Chirality restraints: 1800 Sorted by residual: chirality pdb=" CB THR A 42 " pdb=" CA THR A 42 " pdb=" OG1 THR A 42 " pdb=" CG2 THR A 42 " both_signs ideal model delta sigma weight residual False 2.55 2.10 0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" CB THR I 42 " pdb=" CA THR I 42 " pdb=" OG1 THR I 42 " pdb=" CG2 THR I 42 " both_signs ideal model delta sigma weight residual False 2.55 2.10 0.46 2.00e-01 2.50e+01 5.18e+00 chirality pdb=" CB THR E 42 " pdb=" CA THR E 42 " pdb=" OG1 THR E 42 " pdb=" CG2 THR E 42 " both_signs ideal model delta sigma weight residual False 2.55 2.10 0.45 2.00e-01 2.50e+01 5.16e+00 ... (remaining 1797 not shown) Planarity restraints: 2262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K 165 " 0.054 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO K 166 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO K 166 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO K 166 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 165 " 0.054 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO D 166 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO D 166 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 166 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 165 " 0.054 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO G 166 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO G 166 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO G 166 " 0.046 5.00e-02 4.00e+02 ... (remaining 2259 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3648 2.81 - 3.33: 11956 3.33 - 3.85: 21151 3.85 - 4.38: 24087 4.38 - 4.90: 40105 Nonbonded interactions: 100947 Sorted by model distance: nonbonded pdb=" OE2 GLU C 34 " pdb=" NH1 ARG G 182 " model vdw 2.286 2.520 nonbonded pdb=" OE2 GLU H 34 " pdb=" NH1 ARG K 182 " model vdw 2.286 2.520 nonbonded pdb=" NH1 ARG D 182 " pdb=" OE2 GLU L 34 " model vdw 2.287 2.520 nonbonded pdb=" N ASP K 184 " pdb=" O PRO K 204 " model vdw 2.295 2.520 nonbonded pdb=" N ASP G 184 " pdb=" O PRO G 204 " model vdw 2.295 2.520 ... (remaining 100942 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 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.020 Extract box with map and model: 6.100 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 32.510 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 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 : 0.007 0.057 12432 Z= 0.431 Angle : 1.138 15.287 16824 Z= 0.618 Chirality : 0.073 0.455 1800 Planarity : 0.008 0.083 2262 Dihedral : 13.672 77.369 4422 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 16.73 % Favored : 83.07 % Rotamer: Outliers : 1.20 % Allowed : 9.62 % Favored : 89.18 % 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: -5.28 (0.16), residues: 1536 helix: -3.58 (0.29), residues: 174 sheet: -2.92 (0.20), residues: 462 loop : -3.98 (0.15), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 81 HIS 0.006 0.001 HIS C 74 PHE 0.029 0.003 PHE H 76 TYR 0.008 0.002 TYR F 122 ARG 0.007 0.001 ARG J 60 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 642 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ASN cc_start: 0.7749 (t0) cc_final: 0.7520 (t0) REVERT: A 9 LEU cc_start: 0.7887 (pp) cc_final: 0.7631 (pp) REVERT: A 11 ILE cc_start: 0.8565 (pt) cc_final: 0.8175 (mp) REVERT: A 24 ILE cc_start: 0.8985 (pt) cc_final: 0.8452 (tp) REVERT: A 92 GLN cc_start: 0.8839 (tt0) cc_final: 0.8501 (tt0) REVERT: A 93 VAL cc_start: 0.8806 (t) cc_final: 0.8604 (p) REVERT: A 111 ASP cc_start: 0.8477 (p0) cc_final: 0.7770 (p0) REVERT: A 124 LEU cc_start: 0.8849 (tt) cc_final: 0.8451 (tp) REVERT: B 9 LEU cc_start: 0.8382 (pp) cc_final: 0.8083 (pt) REVERT: B 24 ILE cc_start: 0.8751 (pt) cc_final: 0.7902 (tp) REVERT: B 43 SER cc_start: 0.7755 (p) cc_final: 0.6658 (t) REVERT: B 71 LYS cc_start: 0.8643 (mtmt) cc_final: 0.8365 (mtmt) REVERT: B 85 ASP cc_start: 0.8801 (m-30) cc_final: 0.8113 (t0) REVERT: B 91 PHE cc_start: 0.8565 (m-80) cc_final: 0.8242 (m-10) REVERT: B 92 GLN cc_start: 0.8856 (tt0) cc_final: 0.8640 (tt0) REVERT: B 124 LEU cc_start: 0.8916 (tt) cc_final: 0.8073 (tt) REVERT: D 57 ASP cc_start: 0.8641 (t0) cc_final: 0.7946 (t0) REVERT: D 66 PHE cc_start: 0.9250 (t80) cc_final: 0.8944 (t80) REVERT: D 207 GLU cc_start: 0.7832 (pp20) cc_final: 0.7569 (pp20) REVERT: C 37 ASN cc_start: 0.8670 (t0) cc_final: 0.7788 (t0) REVERT: C 208 VAL cc_start: 0.8755 (t) cc_final: 0.8496 (t) REVERT: E 9 LEU cc_start: 0.8024 (pp) cc_final: 0.7796 (pt) REVERT: E 11 ILE cc_start: 0.8663 (pt) cc_final: 0.8385 (mp) REVERT: E 24 ILE cc_start: 0.9031 (pt) cc_final: 0.8323 (tp) REVERT: E 92 GLN cc_start: 0.8821 (tt0) cc_final: 0.7443 (tt0) REVERT: E 100 ILE cc_start: 0.8046 (pt) cc_final: 0.7792 (pt) REVERT: E 102 GLN cc_start: 0.7609 (tp-100) cc_final: 0.7313 (tp40) REVERT: E 111 ASP cc_start: 0.8645 (p0) cc_final: 0.8311 (p0) REVERT: E 124 LEU cc_start: 0.8907 (tt) cc_final: 0.8485 (tp) REVERT: F 4 GLN cc_start: 0.7087 (mm-40) cc_final: 0.6839 (mp10) REVERT: F 9 LEU cc_start: 0.8179 (pp) cc_final: 0.7848 (pt) REVERT: F 24 ILE cc_start: 0.8729 (pt) cc_final: 0.7939 (tp) REVERT: F 42 THR cc_start: 0.9172 (t) cc_final: 0.8941 (m) REVERT: F 43 SER cc_start: 0.7806 (p) cc_final: 0.6740 (t) REVERT: F 71 LYS cc_start: 0.8678 (mtmt) cc_final: 0.8235 (mtpp) REVERT: F 77 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8327 (tp30) REVERT: F 80 ARG cc_start: 0.8652 (tmm160) cc_final: 0.8299 (tmm160) REVERT: F 85 ASP cc_start: 0.8621 (m-30) cc_final: 0.8175 (t0) REVERT: F 91 PHE cc_start: 0.8534 (m-80) cc_final: 0.8079 (m-10) REVERT: F 92 GLN cc_start: 0.8681 (tt0) cc_final: 0.8390 (tt0) REVERT: F 124 LEU cc_start: 0.9121 (tt) cc_final: 0.8746 (tp) REVERT: G 66 PHE cc_start: 0.9222 (t80) cc_final: 0.8848 (t80) REVERT: G 207 GLU cc_start: 0.7829 (pp20) cc_final: 0.7624 (pp20) REVERT: H 37 ASN cc_start: 0.8726 (t0) cc_final: 0.8219 (t0) REVERT: I 9 LEU cc_start: 0.7889 (pp) cc_final: 0.7633 (pt) REVERT: I 11 ILE cc_start: 0.8618 (pt) cc_final: 0.8296 (mp) REVERT: I 24 ILE cc_start: 0.9003 (pt) cc_final: 0.8252 (tp) REVERT: I 81 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8234 (tp40) REVERT: I 85 ASP cc_start: 0.9045 (m-30) cc_final: 0.8324 (m-30) REVERT: I 92 GLN cc_start: 0.8810 (tt0) cc_final: 0.7431 (tt0) REVERT: I 102 GLN cc_start: 0.7511 (tp-100) cc_final: 0.7018 (tp40) REVERT: I 111 ASP cc_start: 0.8464 (p0) cc_final: 0.7797 (p0) REVERT: I 124 LEU cc_start: 0.8854 (tt) cc_final: 0.8322 (tp) REVERT: J 8 ASP cc_start: 0.7849 (m-30) cc_final: 0.7572 (t70) REVERT: J 9 LEU cc_start: 0.8083 (pp) cc_final: 0.7535 (pp) REVERT: J 24 ILE cc_start: 0.8733 (pt) cc_final: 0.7897 (tp) REVERT: J 43 SER cc_start: 0.7769 (p) cc_final: 0.6948 (t) REVERT: J 71 LYS cc_start: 0.8519 (mtmt) cc_final: 0.8130 (mtpp) REVERT: J 77 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8216 (tp30) REVERT: J 80 ARG cc_start: 0.8632 (tmm160) cc_final: 0.8386 (tmm160) REVERT: J 85 ASP cc_start: 0.8780 (m-30) cc_final: 0.8295 (t0) REVERT: J 91 PHE cc_start: 0.8502 (m-80) cc_final: 0.7952 (m-10) REVERT: J 92 GLN cc_start: 0.8817 (tt0) cc_final: 0.8441 (tt0) REVERT: K 66 PHE cc_start: 0.9298 (t80) cc_final: 0.8980 (t80) REVERT: L 37 ASN cc_start: 0.8629 (t0) cc_final: 0.8005 (t0) REVERT: L 66 PHE cc_start: 0.9199 (t80) cc_final: 0.8908 (t80) outliers start: 15 outliers final: 1 residues processed: 653 average time/residue: 0.2685 time to fit residues: 240.0432 Evaluate side-chains 441 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 440 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 91 optimal weight: 0.0010 chunk 141 optimal weight: 0.7980 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 167 GLN E 20 GLN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN H 167 GLN I 20 GLN ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 167 GLN L 72 GLN L 167 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12432 Z= 0.246 Angle : 0.808 10.807 16824 Z= 0.418 Chirality : 0.051 0.176 1800 Planarity : 0.008 0.079 2262 Dihedral : 7.378 28.319 1698 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 26.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.15 % Favored : 86.85 % Rotamer: Outliers : 1.04 % Allowed : 5.53 % Favored : 93.43 % 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: -4.68 (0.17), residues: 1536 helix: -2.89 (0.32), residues: 180 sheet: -2.65 (0.21), residues: 432 loop : -3.54 (0.16), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP G 78 HIS 0.008 0.002 HIS C 74 PHE 0.021 0.002 PHE L 76 TYR 0.012 0.002 TYR B 112 ARG 0.008 0.001 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 505 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 VAL cc_start: 0.8811 (t) cc_final: 0.8553 (p) REVERT: A 81 GLN cc_start: 0.8994 (tp40) cc_final: 0.8243 (tp40) REVERT: A 82 ILE cc_start: 0.9323 (tp) cc_final: 0.9117 (tp) REVERT: A 85 ASP cc_start: 0.9094 (m-30) cc_final: 0.8139 (m-30) REVERT: A 92 GLN cc_start: 0.8646 (tt0) cc_final: 0.8443 (tt0) REVERT: B 77 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8675 (tp30) REVERT: B 82 ILE cc_start: 0.9199 (tp) cc_final: 0.8955 (tp) REVERT: B 85 ASP cc_start: 0.8683 (m-30) cc_final: 0.8024 (m-30) REVERT: D 57 ASP cc_start: 0.8675 (t0) cc_final: 0.7742 (t0) REVERT: C 37 ASN cc_start: 0.8357 (t0) cc_final: 0.7849 (t0) REVERT: C 60 GLU cc_start: 0.8580 (mm-30) cc_final: 0.7601 (pt0) REVERT: C 186 ASP cc_start: 0.8118 (p0) cc_final: 0.7881 (p0) REVERT: E 35 ASN cc_start: 0.9188 (m-40) cc_final: 0.8414 (p0) REVERT: E 52 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7905 (mp0) REVERT: E 53 LEU cc_start: 0.8930 (mp) cc_final: 0.8493 (mm) REVERT: E 78 ARG cc_start: 0.8741 (tpt-90) cc_final: 0.8447 (tpt-90) REVERT: E 81 GLN cc_start: 0.8989 (tp40) cc_final: 0.8187 (tp40) REVERT: E 82 ILE cc_start: 0.9292 (tp) cc_final: 0.8971 (tp) REVERT: E 85 ASP cc_start: 0.9044 (m-30) cc_final: 0.8242 (m-30) REVERT: E 92 GLN cc_start: 0.8635 (tt0) cc_final: 0.8366 (tt0) REVERT: E 102 GLN cc_start: 0.7994 (tp-100) cc_final: 0.7786 (tp40) REVERT: F 42 THR cc_start: 0.9330 (t) cc_final: 0.9098 (m) REVERT: F 77 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8515 (tp30) REVERT: F 82 ILE cc_start: 0.9327 (tp) cc_final: 0.8679 (tp) REVERT: F 85 ASP cc_start: 0.8564 (m-30) cc_final: 0.8304 (t0) REVERT: F 87 GLU cc_start: 0.7951 (mp0) cc_final: 0.7632 (mp0) REVERT: G 56 LEU cc_start: 0.9188 (mm) cc_final: 0.8851 (mm) REVERT: G 57 ASP cc_start: 0.8697 (t70) cc_final: 0.8442 (t0) REVERT: H 37 ASN cc_start: 0.8427 (t0) cc_final: 0.7717 (t0) REVERT: H 60 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7452 (pt0) REVERT: I 78 ARG cc_start: 0.8592 (tpt-90) cc_final: 0.8364 (tpt-90) REVERT: I 92 GLN cc_start: 0.8476 (tt0) cc_final: 0.8144 (tt0) REVERT: I 102 GLN cc_start: 0.7835 (tp-100) cc_final: 0.7300 (mm110) REVERT: I 106 MET cc_start: 0.8497 (ptp) cc_final: 0.8195 (ptp) REVERT: I 111 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7629 (p0) REVERT: J 5 ASN cc_start: 0.8253 (t0) cc_final: 0.8002 (t0) REVERT: J 35 ASN cc_start: 0.9372 (m-40) cc_final: 0.9136 (m-40) REVERT: J 77 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8385 (tp30) REVERT: J 82 ILE cc_start: 0.9254 (tp) cc_final: 0.8587 (tp) REVERT: J 85 ASP cc_start: 0.8599 (m-30) cc_final: 0.8246 (t0) REVERT: J 87 GLU cc_start: 0.7958 (mp0) cc_final: 0.7600 (mp0) REVERT: J 98 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6161 (m-10) REVERT: J 108 THR cc_start: 0.8818 (p) cc_final: 0.8593 (p) REVERT: L 37 ASN cc_start: 0.8330 (t0) cc_final: 0.8065 (t0) REVERT: L 67 GLU cc_start: 0.7387 (tm-30) cc_final: 0.7144 (tm-30) REVERT: L 193 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8100 (pt0) outliers start: 13 outliers final: 0 residues processed: 511 average time/residue: 0.2725 time to fit residues: 189.9782 Evaluate side-chains 398 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 396 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.0570 chunk 43 optimal weight: 8.9990 chunk 117 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 141 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN D 167 GLN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN E 20 GLN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN ** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 GLN I 20 GLN ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 GLN K 167 GLN L 167 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12432 Z= 0.216 Angle : 0.777 8.524 16824 Z= 0.401 Chirality : 0.050 0.218 1800 Planarity : 0.007 0.061 2262 Dihedral : 6.838 28.661 1698 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 26.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer: Outliers : 0.48 % Allowed : 7.21 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.18), residues: 1536 helix: -2.57 (0.34), residues: 180 sheet: -2.34 (0.24), residues: 384 loop : -3.35 (0.17), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 78 HIS 0.006 0.001 HIS L 74 PHE 0.039 0.002 PHE D 76 TYR 0.012 0.002 TYR K 47 ARG 0.009 0.001 ARG I 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 467 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.9203 (m-40) cc_final: 0.8513 (p0) REVERT: A 41 VAL cc_start: 0.8817 (t) cc_final: 0.8506 (p) REVERT: A 52 GLU cc_start: 0.7791 (mp0) cc_final: 0.7078 (mp0) REVERT: A 81 GLN cc_start: 0.8970 (tp40) cc_final: 0.8387 (tp40) REVERT: A 82 ILE cc_start: 0.9053 (tp) cc_final: 0.8669 (tp) REVERT: A 85 ASP cc_start: 0.9012 (m-30) cc_final: 0.8337 (m-30) REVERT: A 107 ILE cc_start: 0.9221 (tp) cc_final: 0.8508 (tp) REVERT: A 124 LEU cc_start: 0.9014 (tt) cc_final: 0.8503 (tt) REVERT: B 77 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8698 (tp30) REVERT: B 82 ILE cc_start: 0.9273 (tp) cc_final: 0.8423 (pt) REVERT: B 111 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7973 (p0) REVERT: D 57 ASP cc_start: 0.8753 (t0) cc_final: 0.8500 (t0) REVERT: C 25 GLU cc_start: 0.9058 (pm20) cc_final: 0.8697 (pm20) REVERT: C 37 ASN cc_start: 0.8368 (t0) cc_final: 0.7773 (t0) REVERT: C 60 GLU cc_start: 0.8588 (mm-30) cc_final: 0.7627 (pt0) REVERT: C 193 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8324 (pt0) REVERT: E 35 ASN cc_start: 0.9243 (m-40) cc_final: 0.8601 (p0) REVERT: E 52 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7818 (mp0) REVERT: E 53 LEU cc_start: 0.8361 (mp) cc_final: 0.8127 (mt) REVERT: E 81 GLN cc_start: 0.8932 (tp40) cc_final: 0.8310 (tp40) REVERT: E 82 ILE cc_start: 0.9114 (tp) cc_final: 0.8850 (tp) REVERT: E 85 ASP cc_start: 0.8784 (m-30) cc_final: 0.8091 (m-30) REVERT: E 92 GLN cc_start: 0.8502 (tt0) cc_final: 0.8224 (tt0) REVERT: F 77 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8497 (tp30) REVERT: G 57 ASP cc_start: 0.8589 (t70) cc_final: 0.8190 (t0) REVERT: H 25 GLU cc_start: 0.8874 (pm20) cc_final: 0.8603 (pm20) REVERT: H 37 ASN cc_start: 0.8414 (t0) cc_final: 0.7609 (t0) REVERT: H 60 GLU cc_start: 0.8595 (mm-30) cc_final: 0.7568 (pt0) REVERT: H 186 ASP cc_start: 0.8074 (p0) cc_final: 0.7327 (p0) REVERT: H 187 ARG cc_start: 0.8498 (ptp90) cc_final: 0.8069 (ptp90) REVERT: H 193 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8016 (pt0) REVERT: I 52 GLU cc_start: 0.7527 (mp0) cc_final: 0.7302 (mp0) REVERT: I 92 GLN cc_start: 0.8490 (tt0) cc_final: 0.8228 (tt0) REVERT: I 102 GLN cc_start: 0.8006 (tp-100) cc_final: 0.7555 (mm110) REVERT: I 107 ILE cc_start: 0.9254 (tp) cc_final: 0.9035 (tp) REVERT: J 5 ASN cc_start: 0.8312 (t0) cc_final: 0.8022 (t0) REVERT: J 35 ASN cc_start: 0.9363 (m-40) cc_final: 0.8520 (p0) REVERT: J 77 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8427 (tp30) REVERT: J 107 ILE cc_start: 0.9285 (tt) cc_final: 0.9045 (tt) REVERT: L 37 ASN cc_start: 0.8351 (t0) cc_final: 0.8034 (t0) REVERT: L 193 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8104 (pt0) outliers start: 6 outliers final: 0 residues processed: 472 average time/residue: 0.2480 time to fit residues: 164.3617 Evaluate side-chains 378 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 377 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 150 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 HIS B 116 HIS D 193 GLN ** C 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN F 20 GLN F 92 GLN F 116 HIS ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN I 20 GLN ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 HIS J 20 GLN J 116 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12432 Z= 0.368 Angle : 0.845 8.570 16824 Z= 0.445 Chirality : 0.052 0.245 1800 Planarity : 0.008 0.094 2262 Dihedral : 7.240 30.623 1698 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 31.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.67 % Favored : 86.33 % Rotamer: Outliers : 0.56 % Allowed : 7.77 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % 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 (0.19), residues: 1536 helix: -2.52 (0.33), residues: 174 sheet: -2.43 (0.22), residues: 414 loop : -3.13 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP C 78 HIS 0.007 0.002 HIS C 74 PHE 0.038 0.003 PHE G 76 TYR 0.013 0.002 TYR C 47 ARG 0.008 0.001 ARG L 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 466 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.9259 (m-40) cc_final: 0.8497 (p0) REVERT: A 41 VAL cc_start: 0.8773 (t) cc_final: 0.8343 (p) REVERT: A 52 GLU cc_start: 0.7854 (mp0) cc_final: 0.7176 (mp0) REVERT: A 87 GLU cc_start: 0.8590 (pm20) cc_final: 0.8066 (pm20) REVERT: A 92 GLN cc_start: 0.8679 (tt0) cc_final: 0.8408 (tt0) REVERT: B 35 ASN cc_start: 0.8851 (m110) cc_final: 0.8448 (m-40) REVERT: D 23 ARG cc_start: 0.7945 (tpp-160) cc_final: 0.7711 (tpp-160) REVERT: D 57 ASP cc_start: 0.8760 (t0) cc_final: 0.8538 (t0) REVERT: C 57 ASP cc_start: 0.8993 (t0) cc_final: 0.8769 (t0) REVERT: C 60 GLU cc_start: 0.8764 (mm-30) cc_final: 0.7789 (pt0) REVERT: E 35 ASN cc_start: 0.9217 (m-40) cc_final: 0.8568 (p0) REVERT: E 52 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7563 (mp0) REVERT: E 82 ILE cc_start: 0.9408 (tp) cc_final: 0.9108 (tp) REVERT: E 102 GLN cc_start: 0.8539 (tp40) cc_final: 0.7828 (mm110) REVERT: F 53 LEU cc_start: 0.8370 (mp) cc_final: 0.8155 (mp) REVERT: G 57 ASP cc_start: 0.8728 (t70) cc_final: 0.8431 (t0) REVERT: H 57 ASP cc_start: 0.8931 (t0) cc_final: 0.8563 (t0) REVERT: H 60 GLU cc_start: 0.8630 (mm-30) cc_final: 0.7767 (pt0) REVERT: I 30 THR cc_start: 0.8809 (t) cc_final: 0.8591 (m) REVERT: I 52 GLU cc_start: 0.7663 (mp0) cc_final: 0.7140 (mp0) REVERT: I 85 ASP cc_start: 0.9250 (m-30) cc_final: 0.8846 (m-30) REVERT: I 92 GLN cc_start: 0.8570 (tt0) cc_final: 0.7766 (tt0) REVERT: I 100 ILE cc_start: 0.8397 (pt) cc_final: 0.7999 (pt) REVERT: I 102 GLN cc_start: 0.8114 (tp-100) cc_final: 0.7822 (tp40) REVERT: I 107 ILE cc_start: 0.9337 (tp) cc_final: 0.8891 (tp) REVERT: I 124 LEU cc_start: 0.9054 (tt) cc_final: 0.8338 (tt) REVERT: J 35 ASN cc_start: 0.9335 (m-40) cc_final: 0.8311 (p0) REVERT: J 63 SER cc_start: 0.9248 (m) cc_final: 0.8855 (p) REVERT: J 82 ILE cc_start: 0.9166 (tp) cc_final: 0.8539 (tp) REVERT: J 85 ASP cc_start: 0.8408 (t0) cc_final: 0.8184 (t0) REVERT: L 67 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7685 (tm-30) outliers start: 7 outliers final: 2 residues processed: 473 average time/residue: 0.2381 time to fit residues: 160.2734 Evaluate side-chains 369 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 367 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 135 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN E 20 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12432 Z= 0.347 Angle : 0.848 8.623 16824 Z= 0.441 Chirality : 0.052 0.193 1800 Planarity : 0.008 0.081 2262 Dihedral : 7.169 31.766 1698 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 31.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % Rotamer: Outliers : 0.40 % Allowed : 5.53 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.04 (0.19), residues: 1536 helix: -2.30 (0.32), residues: 174 sheet: -2.33 (0.23), residues: 414 loop : -3.06 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 50 HIS 0.008 0.002 HIS C 74 PHE 0.035 0.002 PHE D 76 TYR 0.019 0.002 TYR H 47 ARG 0.009 0.001 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 433 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.9245 (m-40) cc_final: 0.8609 (p0) REVERT: A 41 VAL cc_start: 0.8719 (t) cc_final: 0.8272 (p) REVERT: A 52 GLU cc_start: 0.7815 (mp0) cc_final: 0.7131 (mp0) REVERT: A 87 GLU cc_start: 0.8672 (pm20) cc_final: 0.7964 (pm20) REVERT: A 92 GLN cc_start: 0.8677 (tt0) cc_final: 0.8456 (tt0) REVERT: A 123 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8299 (mt-10) REVERT: A 124 LEU cc_start: 0.9066 (tt) cc_final: 0.8656 (tt) REVERT: B 82 ILE cc_start: 0.9373 (tp) cc_final: 0.9125 (tp) REVERT: B 102 GLN cc_start: 0.8644 (tp40) cc_final: 0.8038 (tp40) REVERT: C 193 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8324 (mp10) REVERT: E 35 ASN cc_start: 0.9193 (m-40) cc_final: 0.8559 (p0) REVERT: E 52 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7438 (mp0) REVERT: E 92 GLN cc_start: 0.8612 (tt0) cc_final: 0.7900 (tt0) REVERT: E 100 ILE cc_start: 0.8631 (pt) cc_final: 0.8106 (pt) REVERT: E 102 GLN cc_start: 0.8867 (tp40) cc_final: 0.7299 (tp40) REVERT: E 134 PHE cc_start: 0.7654 (m-80) cc_final: 0.7028 (m-10) REVERT: F 82 ILE cc_start: 0.9449 (tp) cc_final: 0.9007 (tp) REVERT: F 85 ASP cc_start: 0.8406 (t0) cc_final: 0.8116 (t0) REVERT: G 69 ARG cc_start: 0.7051 (ptp90) cc_final: 0.6798 (ptp90) REVERT: H 57 ASP cc_start: 0.8914 (t0) cc_final: 0.8456 (t0) REVERT: H 60 GLU cc_start: 0.8648 (mm-30) cc_final: 0.7697 (pt0) REVERT: H 67 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7386 (tm-30) REVERT: I 52 GLU cc_start: 0.7631 (mp0) cc_final: 0.7161 (mp0) REVERT: I 85 ASP cc_start: 0.9264 (m-30) cc_final: 0.8884 (m-30) REVERT: I 92 GLN cc_start: 0.8523 (tt0) cc_final: 0.7593 (tt0) REVERT: I 100 ILE cc_start: 0.8520 (pt) cc_final: 0.8188 (pt) REVERT: I 102 GLN cc_start: 0.8355 (tp-100) cc_final: 0.7959 (tp40) REVERT: I 107 ILE cc_start: 0.9339 (tp) cc_final: 0.9075 (tp) REVERT: J 35 ASN cc_start: 0.9381 (m-40) cc_final: 0.8862 (m-40) REVERT: J 63 SER cc_start: 0.9225 (m) cc_final: 0.8825 (p) REVERT: J 111 ASP cc_start: 0.8534 (p0) cc_final: 0.8147 (p0) REVERT: K 54 ARG cc_start: 0.7804 (pmt170) cc_final: 0.7597 (pmt-80) REVERT: L 53 LEU cc_start: 0.6918 (mt) cc_final: 0.6549 (mt) REVERT: L 67 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7624 (tm-30) outliers start: 5 outliers final: 0 residues processed: 438 average time/residue: 0.2407 time to fit residues: 149.8430 Evaluate side-chains 350 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 0.1980 chunk 79 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 GLN ** C 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN E 20 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN H 74 HIS I 20 GLN ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN K 167 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.6850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12432 Z= 0.262 Angle : 0.829 10.845 16824 Z= 0.423 Chirality : 0.052 0.205 1800 Planarity : 0.007 0.077 2262 Dihedral : 6.941 30.695 1698 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 27.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % Rotamer: Outliers : 0.40 % Allowed : 4.41 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.98 (0.19), residues: 1536 helix: -2.12 (0.33), residues: 174 sheet: -2.24 (0.23), residues: 414 loop : -3.08 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 78 HIS 0.008 0.002 HIS C 74 PHE 0.030 0.002 PHE D 76 TYR 0.014 0.002 TYR H 47 ARG 0.014 0.001 ARG L 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 440 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.9240 (m-40) cc_final: 0.8592 (p0) REVERT: A 41 VAL cc_start: 0.8714 (t) cc_final: 0.8280 (p) REVERT: A 52 GLU cc_start: 0.7873 (mp0) cc_final: 0.7162 (mp0) REVERT: A 85 ASP cc_start: 0.9121 (m-30) cc_final: 0.7866 (p0) REVERT: A 87 GLU cc_start: 0.8576 (pm20) cc_final: 0.7461 (pm20) REVERT: B 22 GLU cc_start: 0.8159 (mp0) cc_final: 0.7934 (mp0) REVERT: B 63 SER cc_start: 0.9224 (m) cc_final: 0.8742 (p) REVERT: B 102 GLN cc_start: 0.8613 (tp40) cc_final: 0.8065 (tp40) REVERT: D 53 LEU cc_start: 0.6503 (mt) cc_final: 0.6239 (mt) REVERT: D 69 ARG cc_start: 0.6941 (ptp90) cc_final: 0.6521 (ptp90) REVERT: C 60 GLU cc_start: 0.8705 (mm-30) cc_final: 0.7676 (pt0) REVERT: C 193 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8336 (mp10) REVERT: E 52 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7476 (mp0) REVERT: E 87 GLU cc_start: 0.8530 (pm20) cc_final: 0.8241 (pm20) REVERT: E 100 ILE cc_start: 0.8658 (pt) cc_final: 0.7925 (pt) REVERT: E 102 GLN cc_start: 0.8868 (tp40) cc_final: 0.7951 (tp40) REVERT: E 134 PHE cc_start: 0.7880 (m-80) cc_final: 0.7112 (m-10) REVERT: F 35 ASN cc_start: 0.8898 (m110) cc_final: 0.8680 (m-40) REVERT: F 85 ASP cc_start: 0.8828 (t0) cc_final: 0.8471 (t0) REVERT: F 112 TYR cc_start: 0.8317 (m-80) cc_final: 0.8062 (m-80) REVERT: G 69 ARG cc_start: 0.7057 (ptp90) cc_final: 0.6608 (ptp90) REVERT: H 57 ASP cc_start: 0.8968 (t0) cc_final: 0.8595 (t0) REVERT: H 67 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7495 (tm-30) REVERT: I 52 GLU cc_start: 0.7674 (mp0) cc_final: 0.7210 (mp0) REVERT: I 92 GLN cc_start: 0.8446 (tt0) cc_final: 0.8110 (tt0) REVERT: I 102 GLN cc_start: 0.8397 (tp-100) cc_final: 0.8135 (mm110) REVERT: I 107 ILE cc_start: 0.8561 (tp) cc_final: 0.8150 (tp) REVERT: J 22 GLU cc_start: 0.8193 (mp0) cc_final: 0.7975 (mp0) REVERT: J 35 ASN cc_start: 0.9020 (m-40) cc_final: 0.8329 (p0) REVERT: J 63 SER cc_start: 0.9215 (m) cc_final: 0.8825 (p) REVERT: L 67 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7531 (tm-30) outliers start: 5 outliers final: 0 residues processed: 445 average time/residue: 0.2445 time to fit residues: 156.5400 Evaluate side-chains 355 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 150 optimal weight: 7.9990 chunk 94 optimal weight: 0.0470 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 GLN ** C 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN E 20 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN F 92 GLN G 167 GLN ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN K 167 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.6981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12432 Z= 0.229 Angle : 0.814 9.986 16824 Z= 0.413 Chirality : 0.051 0.252 1800 Planarity : 0.007 0.064 2262 Dihedral : 6.672 32.476 1698 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 25.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.09 % Favored : 86.91 % Rotamer: Outliers : 0.40 % Allowed : 3.29 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.80 (0.19), residues: 1536 helix: -1.96 (0.34), residues: 180 sheet: -2.24 (0.24), residues: 402 loop : -2.91 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 40 HIS 0.007 0.001 HIS L 74 PHE 0.030 0.002 PHE C 76 TYR 0.013 0.001 TYR H 47 ARG 0.011 0.001 ARG L 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 435 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.9253 (m-40) cc_final: 0.8711 (p0) REVERT: A 41 VAL cc_start: 0.8725 (t) cc_final: 0.8272 (p) REVERT: A 52 GLU cc_start: 0.7919 (mp0) cc_final: 0.7233 (mp0) REVERT: A 85 ASP cc_start: 0.9119 (m-30) cc_final: 0.7994 (p0) REVERT: A 87 GLU cc_start: 0.8404 (pm20) cc_final: 0.7931 (pm20) REVERT: A 107 ILE cc_start: 0.9081 (tp) cc_final: 0.8749 (tp) REVERT: A 124 LEU cc_start: 0.9115 (tt) cc_final: 0.8836 (tt) REVERT: B 30 THR cc_start: 0.8806 (t) cc_final: 0.8587 (m) REVERT: B 35 ASN cc_start: 0.8625 (m110) cc_final: 0.8399 (m110) REVERT: B 63 SER cc_start: 0.9250 (m) cc_final: 0.8778 (p) REVERT: B 77 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8658 (tp30) REVERT: B 102 GLN cc_start: 0.8587 (tp40) cc_final: 0.8017 (tp40) REVERT: D 53 LEU cc_start: 0.6655 (mt) cc_final: 0.6438 (mt) REVERT: D 57 ASP cc_start: 0.8656 (t0) cc_final: 0.8377 (t0) REVERT: D 69 ARG cc_start: 0.6819 (ptp90) cc_final: 0.6464 (ptp90) REVERT: D 187 ARG cc_start: 0.8093 (ptp90) cc_final: 0.7752 (ptp-170) REVERT: C 60 GLU cc_start: 0.8628 (mm-30) cc_final: 0.7560 (pt0) REVERT: C 193 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8407 (mp10) REVERT: C 202 GLN cc_start: 0.8381 (pm20) cc_final: 0.8156 (pm20) REVERT: E 52 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7391 (mp0) REVERT: E 81 GLN cc_start: 0.9009 (tp40) cc_final: 0.8334 (tp40) REVERT: E 82 ILE cc_start: 0.9402 (tp) cc_final: 0.9178 (tp) REVERT: E 85 ASP cc_start: 0.8930 (m-30) cc_final: 0.8428 (m-30) REVERT: E 92 GLN cc_start: 0.8282 (tt0) cc_final: 0.7238 (tt0) REVERT: E 100 ILE cc_start: 0.8592 (pt) cc_final: 0.8122 (pt) REVERT: E 102 GLN cc_start: 0.8879 (tp40) cc_final: 0.7512 (tp40) REVERT: E 124 LEU cc_start: 0.9169 (tt) cc_final: 0.8725 (tt) REVERT: E 134 PHE cc_start: 0.7604 (m-80) cc_final: 0.7025 (m-10) REVERT: F 35 ASN cc_start: 0.8801 (m110) cc_final: 0.8487 (m-40) REVERT: F 85 ASP cc_start: 0.8815 (t0) cc_final: 0.8451 (t0) REVERT: G 69 ARG cc_start: 0.7032 (ptp90) cc_final: 0.6483 (ptp90) REVERT: H 57 ASP cc_start: 0.8908 (t0) cc_final: 0.8536 (t0) REVERT: H 67 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7392 (tm-30) REVERT: I 52 GLU cc_start: 0.7677 (mp0) cc_final: 0.7199 (mp0) REVERT: I 92 GLN cc_start: 0.8342 (tt0) cc_final: 0.8079 (tt0) REVERT: I 100 ILE cc_start: 0.8344 (pt) cc_final: 0.8067 (pt) REVERT: I 102 GLN cc_start: 0.8426 (tp-100) cc_final: 0.8153 (mm110) REVERT: I 107 ILE cc_start: 0.9114 (tp) cc_final: 0.8636 (tp) REVERT: I 124 LEU cc_start: 0.8970 (tt) cc_final: 0.8707 (tt) REVERT: J 63 SER cc_start: 0.9169 (m) cc_final: 0.8756 (p) REVERT: L 67 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7130 (tm-30) outliers start: 5 outliers final: 0 residues processed: 440 average time/residue: 0.2419 time to fit residues: 154.0321 Evaluate side-chains 366 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** C 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN F 92 GLN I 20 GLN ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.7404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 12432 Z= 0.466 Angle : 0.962 11.923 16824 Z= 0.500 Chirality : 0.057 0.249 1800 Planarity : 0.009 0.094 2262 Dihedral : 7.431 33.667 1698 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 35.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.15 % Favored : 83.85 % Rotamer: Outliers : 0.40 % Allowed : 2.88 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.94 (0.19), residues: 1536 helix: -2.25 (0.32), residues: 186 sheet: -2.36 (0.24), residues: 402 loop : -2.94 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP L 78 HIS 0.010 0.002 HIS H 4 PHE 0.051 0.003 PHE H 76 TYR 0.015 0.002 TYR H 47 ARG 0.017 0.001 ARG L 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 410 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.9252 (m-40) cc_final: 0.9049 (m-40) REVERT: A 52 GLU cc_start: 0.7879 (mp0) cc_final: 0.6998 (mp0) REVERT: A 85 ASP cc_start: 0.9153 (m-30) cc_final: 0.8511 (m-30) REVERT: A 87 GLU cc_start: 0.8924 (pm20) cc_final: 0.8297 (pm20) REVERT: A 102 GLN cc_start: 0.8659 (mm110) cc_final: 0.8391 (mm110) REVERT: B 63 SER cc_start: 0.9275 (m) cc_final: 0.8797 (p) REVERT: B 77 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8660 (tp30) REVERT: B 102 GLN cc_start: 0.8632 (tp40) cc_final: 0.8143 (tp40) REVERT: C 67 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7588 (tm-30) REVERT: C 207 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8341 (tm-30) REVERT: E 52 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7471 (mp0) REVERT: E 82 ILE cc_start: 0.9434 (tp) cc_final: 0.8970 (tp) REVERT: E 85 ASP cc_start: 0.9150 (m-30) cc_final: 0.7983 (p0) REVERT: E 87 GLU cc_start: 0.8824 (pm20) cc_final: 0.8072 (pm20) REVERT: E 92 GLN cc_start: 0.8409 (tt0) cc_final: 0.7207 (tt0) REVERT: E 100 ILE cc_start: 0.8706 (pt) cc_final: 0.8133 (pt) REVERT: E 102 GLN cc_start: 0.8800 (tp40) cc_final: 0.7501 (tp40) REVERT: E 124 LEU cc_start: 0.9257 (tt) cc_final: 0.8795 (tt) REVERT: E 134 PHE cc_start: 0.8171 (m-80) cc_final: 0.7418 (m-10) REVERT: F 85 ASP cc_start: 0.8909 (t0) cc_final: 0.8508 (t0) REVERT: F 87 GLU cc_start: 0.8579 (pm20) cc_final: 0.8288 (pm20) REVERT: G 57 ASP cc_start: 0.8651 (t70) cc_final: 0.8318 (t0) REVERT: H 57 ASP cc_start: 0.8972 (t0) cc_final: 0.8704 (t0) REVERT: H 67 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7230 (tm-30) REVERT: H 196 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8643 (mm-40) REVERT: I 52 GLU cc_start: 0.7579 (mp0) cc_final: 0.7032 (mp0) REVERT: I 107 ILE cc_start: 0.8788 (tp) cc_final: 0.8334 (tp) REVERT: I 123 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8239 (mm-30) REVERT: J 5 ASN cc_start: 0.8264 (t0) cc_final: 0.8042 (t0) REVERT: J 63 SER cc_start: 0.9246 (m) cc_final: 0.8769 (p) REVERT: J 132 LEU cc_start: 0.8513 (mt) cc_final: 0.8280 (mt) outliers start: 5 outliers final: 0 residues processed: 415 average time/residue: 0.2389 time to fit residues: 140.8103 Evaluate side-chains 343 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN B 20 GLN D 167 GLN ** C 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN E 20 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN F 92 GLN G 167 GLN I 20 GLN ** I 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN J 20 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.7447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12432 Z= 0.250 Angle : 0.877 13.283 16824 Z= 0.445 Chirality : 0.054 0.285 1800 Planarity : 0.007 0.085 2262 Dihedral : 6.862 32.089 1698 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 27.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.96 % Favored : 87.04 % Rotamer: Outliers : 0.48 % Allowed : 0.56 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.81 (0.19), residues: 1536 helix: -1.86 (0.35), residues: 180 sheet: -2.22 (0.24), residues: 402 loop : -2.94 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 78 HIS 0.007 0.001 HIS C 74 PHE 0.040 0.002 PHE H 76 TYR 0.011 0.002 TYR L 47 ARG 0.012 0.001 ARG L 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 425 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.9206 (m-40) cc_final: 0.8782 (p0) REVERT: A 41 VAL cc_start: 0.8769 (t) cc_final: 0.8487 (t) REVERT: A 52 GLU cc_start: 0.7902 (mp0) cc_final: 0.7133 (mp0) REVERT: A 85 ASP cc_start: 0.9082 (m-30) cc_final: 0.8507 (m-30) REVERT: A 87 GLU cc_start: 0.8624 (pm20) cc_final: 0.7995 (pm20) REVERT: A 102 GLN cc_start: 0.8548 (mm110) cc_final: 0.8274 (mm-40) REVERT: A 124 LEU cc_start: 0.9156 (tt) cc_final: 0.8498 (tt) REVERT: B 63 SER cc_start: 0.9232 (m) cc_final: 0.8733 (p) REVERT: B 77 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8676 (tp30) REVERT: B 102 GLN cc_start: 0.8682 (tp40) cc_final: 0.8137 (tp40) REVERT: D 53 LEU cc_start: 0.6576 (mt) cc_final: 0.6297 (mt) REVERT: D 69 ARG cc_start: 0.6915 (ptp90) cc_final: 0.6408 (ptp90) REVERT: D 193 GLN cc_start: 0.6508 (pm20) cc_final: 0.6299 (pm20) REVERT: D 200 LEU cc_start: 0.9432 (pt) cc_final: 0.9228 (pt) REVERT: C 57 ASP cc_start: 0.9006 (t0) cc_final: 0.8767 (t0) REVERT: C 60 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8106 (pt0) REVERT: C 69 ARG cc_start: 0.6790 (ptp90) cc_final: 0.6469 (ptp90) REVERT: C 193 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8280 (mp10) REVERT: E 52 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7478 (mp0) REVERT: E 63 SER cc_start: 0.9230 (m) cc_final: 0.8751 (p) REVERT: E 82 ILE cc_start: 0.9420 (tp) cc_final: 0.8977 (tp) REVERT: E 85 ASP cc_start: 0.9081 (m-30) cc_final: 0.8060 (p0) REVERT: E 87 GLU cc_start: 0.8434 (pm20) cc_final: 0.7817 (pm20) REVERT: E 92 GLN cc_start: 0.8341 (tt0) cc_final: 0.7123 (tt0) REVERT: E 100 ILE cc_start: 0.8625 (pt) cc_final: 0.8023 (pt) REVERT: E 102 GLN cc_start: 0.8837 (tp40) cc_final: 0.7464 (tp40) REVERT: E 132 LEU cc_start: 0.8325 (mt) cc_final: 0.8086 (mt) REVERT: E 134 PHE cc_start: 0.7964 (m-80) cc_final: 0.7272 (m-10) REVERT: F 35 ASN cc_start: 0.8749 (m110) cc_final: 0.8515 (m-40) REVERT: F 63 SER cc_start: 0.9123 (m) cc_final: 0.8634 (p) REVERT: F 85 ASP cc_start: 0.8894 (t0) cc_final: 0.8526 (t0) REVERT: F 112 TYR cc_start: 0.8190 (m-80) cc_final: 0.7949 (m-80) REVERT: G 69 ARG cc_start: 0.7014 (ptp90) cc_final: 0.6621 (ptp90) REVERT: G 76 PHE cc_start: 0.8210 (p90) cc_final: 0.7509 (p90) REVERT: H 57 ASP cc_start: 0.8813 (t0) cc_final: 0.8522 (t0) REVERT: H 67 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7034 (tm-30) REVERT: I 52 GLU cc_start: 0.7550 (mp0) cc_final: 0.7062 (mp0) REVERT: I 102 GLN cc_start: 0.8789 (mm110) cc_final: 0.8017 (mm110) REVERT: I 107 ILE cc_start: 0.9238 (tp) cc_final: 0.8696 (tp) REVERT: I 123 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8201 (mm-30) REVERT: I 124 LEU cc_start: 0.9125 (tt) cc_final: 0.8574 (tt) REVERT: J 63 SER cc_start: 0.9208 (m) cc_final: 0.8742 (p) REVERT: J 85 ASP cc_start: 0.9053 (t0) cc_final: 0.8690 (t0) REVERT: J 132 LEU cc_start: 0.8366 (mt) cc_final: 0.8164 (mt) REVERT: K 202 GLN cc_start: 0.8651 (pm20) cc_final: 0.8391 (pm20) outliers start: 6 outliers final: 0 residues processed: 431 average time/residue: 0.2341 time to fit residues: 144.4096 Evaluate side-chains 361 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN B 20 GLN D 167 GLN ** C 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN E 20 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN F 92 GLN G 167 GLN I 20 GLN ** I 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.7556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12432 Z= 0.236 Angle : 0.867 11.801 16824 Z= 0.435 Chirality : 0.054 0.276 1800 Planarity : 0.007 0.078 2262 Dihedral : 6.642 31.778 1698 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 27.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.74 % Favored : 86.26 % Rotamer: Outliers : 0.48 % Allowed : 0.40 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.69 (0.19), residues: 1536 helix: -1.68 (0.36), residues: 180 sheet: -2.08 (0.25), residues: 402 loop : -2.91 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 78 HIS 0.008 0.001 HIS C 74 PHE 0.041 0.002 PHE H 76 TYR 0.010 0.002 TYR C 47 ARG 0.011 0.001 ARG L 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 412 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 THR cc_start: 0.8878 (t) cc_final: 0.8634 (m) REVERT: A 35 ASN cc_start: 0.9257 (m-40) cc_final: 0.8793 (p0) REVERT: A 41 VAL cc_start: 0.8817 (t) cc_final: 0.8481 (t) REVERT: A 52 GLU cc_start: 0.7981 (mp0) cc_final: 0.7296 (mp0) REVERT: A 85 ASP cc_start: 0.9117 (m-30) cc_final: 0.7771 (p0) REVERT: A 87 GLU cc_start: 0.8504 (pm20) cc_final: 0.7457 (pm20) REVERT: A 124 LEU cc_start: 0.9111 (tt) cc_final: 0.8468 (tt) REVERT: B 20 GLN cc_start: 0.6364 (OUTLIER) cc_final: 0.6142 (pm20) REVERT: B 30 THR cc_start: 0.8787 (t) cc_final: 0.8570 (m) REVERT: B 63 SER cc_start: 0.9258 (m) cc_final: 0.8749 (p) REVERT: B 77 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8700 (tp30) REVERT: B 102 GLN cc_start: 0.8740 (tp40) cc_final: 0.8236 (tp40) REVERT: D 53 LEU cc_start: 0.6419 (mt) cc_final: 0.6162 (mt) REVERT: D 69 ARG cc_start: 0.6934 (ptp90) cc_final: 0.6364 (ptp90) REVERT: D 200 LEU cc_start: 0.9428 (pt) cc_final: 0.9225 (pt) REVERT: C 56 LEU cc_start: 0.9223 (mm) cc_final: 0.8927 (mm) REVERT: C 60 GLU cc_start: 0.8571 (mm-30) cc_final: 0.7958 (pt0) REVERT: C 193 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8335 (mp10) REVERT: E 51 ARG cc_start: 0.8924 (ttp80) cc_final: 0.8612 (ttp80) REVERT: E 52 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7502 (mp0) REVERT: E 53 LEU cc_start: 0.8835 (mp) cc_final: 0.8550 (mp) REVERT: E 63 SER cc_start: 0.9237 (m) cc_final: 0.8759 (p) REVERT: E 82 ILE cc_start: 0.9409 (tp) cc_final: 0.9016 (tp) REVERT: E 85 ASP cc_start: 0.9029 (m-30) cc_final: 0.8091 (p0) REVERT: E 87 GLU cc_start: 0.8235 (pm20) cc_final: 0.7723 (pm20) REVERT: E 92 GLN cc_start: 0.8381 (tt0) cc_final: 0.7144 (tt0) REVERT: E 100 ILE cc_start: 0.8666 (pt) cc_final: 0.8050 (pt) REVERT: E 102 GLN cc_start: 0.8864 (tp40) cc_final: 0.7584 (tp40) REVERT: E 132 LEU cc_start: 0.8347 (mt) cc_final: 0.8119 (mt) REVERT: E 134 PHE cc_start: 0.8085 (m-80) cc_final: 0.7392 (m-10) REVERT: F 35 ASN cc_start: 0.8681 (m110) cc_final: 0.8452 (m-40) REVERT: F 63 SER cc_start: 0.9124 (m) cc_final: 0.8633 (p) REVERT: F 85 ASP cc_start: 0.8891 (t0) cc_final: 0.8565 (t0) REVERT: F 123 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7762 (mm-30) REVERT: F 132 LEU cc_start: 0.8728 (mm) cc_final: 0.8167 (mp) REVERT: G 69 ARG cc_start: 0.7055 (ptp90) cc_final: 0.6573 (ptp90) REVERT: G 76 PHE cc_start: 0.8351 (p90) cc_final: 0.7742 (p90) REVERT: H 57 ASP cc_start: 0.8790 (t0) cc_final: 0.8507 (t0) REVERT: I 52 GLU cc_start: 0.7648 (mp0) cc_final: 0.7147 (mp0) REVERT: I 85 ASP cc_start: 0.9184 (m-30) cc_final: 0.8981 (m-30) REVERT: I 92 GLN cc_start: 0.8412 (tt0) cc_final: 0.7126 (tt0) REVERT: I 102 GLN cc_start: 0.8882 (tp40) cc_final: 0.7782 (tp40) REVERT: I 123 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8111 (mm-30) REVERT: I 124 LEU cc_start: 0.9068 (tt) cc_final: 0.8802 (tt) REVERT: J 63 SER cc_start: 0.9219 (m) cc_final: 0.8757 (p) REVERT: J 85 ASP cc_start: 0.9067 (t0) cc_final: 0.8709 (t0) REVERT: J 132 LEU cc_start: 0.8403 (mt) cc_final: 0.8186 (mt) REVERT: K 207 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8273 (tm-30) outliers start: 6 outliers final: 0 residues processed: 418 average time/residue: 0.2286 time to fit residues: 137.1970 Evaluate side-chains 351 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 350 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 0.0570 chunk 123 optimal weight: 0.2980 chunk 51 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN B 20 GLN D 167 GLN C 11 ASN C 167 GLN E 20 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN F 92 GLN G 167 GLN I 20 GLN ** I 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.102936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.087884 restraints weight = 40776.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.090164 restraints weight = 23093.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.091654 restraints weight = 15043.786| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.7662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12432 Z= 0.221 Angle : 0.868 14.549 16824 Z= 0.432 Chirality : 0.053 0.263 1800 Planarity : 0.007 0.081 2262 Dihedral : 6.504 31.986 1698 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 25.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 0.48 % Allowed : 0.48 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.67 (0.19), residues: 1536 helix: -1.60 (0.37), residues: 180 sheet: -1.53 (0.29), residues: 294 loop : -3.09 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 40 HIS 0.007 0.001 HIS C 74 PHE 0.035 0.002 PHE H 76 TYR 0.008 0.001 TYR L 47 ARG 0.011 0.001 ARG L 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3323.33 seconds wall clock time: 60 minutes 47.60 seconds (3647.60 seconds total)