Starting phenix.real_space_refine on Sun May 3 17:09:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wci_37440/05_2026/8wci_37440.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wci_37440/05_2026/8wci_37440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wci_37440/05_2026/8wci_37440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wci_37440/05_2026/8wci_37440.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wci_37440/05_2026/8wci_37440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wci_37440/05_2026/8wci_37440.map" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 S 85 5.16 5 Na 9 4.78 5 C 9734 2.51 5 N 2208 2.21 5 O 2830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14876 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 1147 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1124 Chain: "B" Number of atoms: 1157 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1112 Chain: "C" Number of atoms: 1149 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1122 Chain: "D" Number of atoms: 1163 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1105 Chain: "E" Number of atoms: 1152 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1118 Chain: "F" Number of atoms: 1152 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1118 Chain: "G" Number of atoms: 1158 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1113 Chain: "H" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain: "I" Number of atoms: 1167 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1103 Chain: "J" Number of atoms: 1158 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1113 Chain: "P" Number of atoms: 2685 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 343, 2677 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 326} Chain breaks: 5 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 Conformer: "B" Number of residues, atoms: 343, 2677 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 326} Chain breaks: 5 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 bond proxies already assigned to first conformer: 2727 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {' NA': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {' NA': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {' NA': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {' NA': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {' NA': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'W3K': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "G" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "H" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "I" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "P" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Residues with excluded nonbonded symmetry interactions: 14 residue: pdb=" N AVAL G 13 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL G 13 " occ=0.50 residue: pdb=" N ALEU G 17 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU G 17 " occ=0.50 residue: pdb=" N ATHR G 21 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR G 21 " occ=0.50 residue: pdb=" N ALEU G 75 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU G 75 " occ=0.50 residue: pdb=" N AVAL I 13 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL I 13 " occ=0.50 residue: pdb=" N ALEU I 17 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU I 17 " occ=0.50 residue: pdb=" N ATHR I 21 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR I 21 " occ=0.50 residue: pdb=" N AGLN I 54 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN I 54 " occ=0.50 residue: pdb=" N ALEU I 75 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU I 75 " occ=0.50 residue: pdb=" N AVAL J 13 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL J 13 " occ=0.50 residue: pdb=" N ALEU J 17 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU J 17 " occ=0.50 residue: pdb=" N ATHR J 21 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR J 21 " occ=0.50 ... (remaining 2 not shown) Time building chain proxies: 6.27, per 1000 atoms: 0.42 Number of scatterers: 14876 At special positions: 0 Unit cell: (123.67, 107.07, 126.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 85 16.00 P 10 15.00 Na 9 11.00 O 2830 8.00 N 2208 7.00 C 9734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 1.0 seconds 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3452 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 1 sheets defined 87.8% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 10 through 46 removed outlier: 4.325A pdb=" N PHE A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 51 through 61 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.898A pdb=" N LEU A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 124 Proline residue: A 98 - end of helix removed outlier: 3.926A pdb=" N GLN A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 137 removed outlier: 4.032A pdb=" N GLY A 131 " --> pdb=" O HIS A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 156 removed outlier: 4.184A pdb=" N ALA A 142 " --> pdb=" O VAL A 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 11 through 46 removed outlier: 3.655A pdb=" N SER B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 63 through 79 removed outlier: 4.016A pdb=" N LEU B 67 " --> pdb=" O GLY B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 124 removed outlier: 3.636A pdb=" N LEU B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Proline residue: B 98 - end of helix removed outlier: 3.756A pdb=" N GLN B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 137 removed outlier: 3.912A pdb=" N GLY B 131 " --> pdb=" O HIS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 156 removed outlier: 4.285A pdb=" N ALA B 142 " --> pdb=" O VAL B 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 11 through 46 removed outlier: 3.762A pdb=" N SER C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 51 through 60 Processing helix chain 'C' and resid 63 through 79 removed outlier: 3.873A pdb=" N LEU C 67 " --> pdb=" O GLY C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 124 Proline residue: C 98 - end of helix removed outlier: 3.721A pdb=" N GLN C 119 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C 120 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 156 removed outlier: 4.166A pdb=" N GLY C 131 " --> pdb=" O HIS C 127 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL C 138 " --> pdb=" O PHE C 134 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N TYR C 141 " --> pdb=" O MET C 137 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA C 142 " --> pdb=" O VAL C 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 8 Processing helix chain 'D' and resid 11 through 46 removed outlier: 3.829A pdb=" N SER D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 63 through 79 removed outlier: 3.820A pdb=" N LEU D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 124 removed outlier: 3.556A pdb=" N LEU D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Proline residue: D 98 - end of helix removed outlier: 3.867A pdb=" N GLN D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 120 " --> pdb=" O ALA D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 137 removed outlier: 3.975A pdb=" N GLY D 131 " --> pdb=" O HIS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 156 removed outlier: 4.123A pdb=" N ALA D 142 " --> pdb=" O VAL D 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 11 through 46 removed outlier: 3.641A pdb=" N SER E 26 " --> pdb=" O ALA E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 50 No H-bonds generated for 'chain 'E' and resid 48 through 50' Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.888A pdb=" N LEU E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 124 Proline residue: E 98 - end of helix removed outlier: 3.756A pdb=" N GLN E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE E 120 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 137 removed outlier: 4.065A pdb=" N GLY E 131 " --> pdb=" O HIS E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 156 removed outlier: 4.257A pdb=" N ALA E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 8 Processing helix chain 'F' and resid 11 through 46 removed outlier: 3.680A pdb=" N SER F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 50 removed outlier: 6.464A pdb=" N GLU F 50 " --> pdb=" O SER F 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 47 through 50' Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 63 through 79 removed outlier: 3.929A pdb=" N LEU F 67 " --> pdb=" O GLY F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 124 removed outlier: 3.571A pdb=" N LEU F 97 " --> pdb=" O LEU F 93 " (cutoff:3.500A) Proline residue: F 98 - end of helix removed outlier: 3.790A pdb=" N GLN F 119 " --> pdb=" O ALA F 115 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE F 120 " --> pdb=" O ALA F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 137 removed outlier: 3.947A pdb=" N GLY F 131 " --> pdb=" O HIS F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 156 removed outlier: 4.227A pdb=" N ALA F 142 " --> pdb=" O VAL F 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 8 Processing helix chain 'G' and resid 11 through 46 removed outlier: 3.645A pdb=" N SER G 26 " --> pdb=" O ALA G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 50 No H-bonds generated for 'chain 'G' and resid 48 through 50' Processing helix chain 'G' and resid 51 through 61 Processing helix chain 'G' and resid 63 through 79 removed outlier: 4.005A pdb=" N LEU G 67 " --> pdb=" O GLY G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 124 Proline residue: G 98 - end of helix removed outlier: 3.779A pdb=" N GLN G 119 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE G 120 " --> pdb=" O ALA G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 137 removed outlier: 3.890A pdb=" N GLY G 131 " --> pdb=" O HIS G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 156 removed outlier: 4.267A pdb=" N ALA G 142 " --> pdb=" O VAL G 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 9 Processing helix chain 'H' and resid 11 through 46 removed outlier: 3.828A pdb=" N SER H 26 " --> pdb=" O ALA H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 50 No H-bonds generated for 'chain 'H' and resid 48 through 50' Processing helix chain 'H' and resid 51 through 61 Processing helix chain 'H' and resid 63 through 79 removed outlier: 4.109A pdb=" N LEU H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 124 removed outlier: 3.586A pdb=" N LEU H 97 " --> pdb=" O LEU H 93 " (cutoff:3.500A) Proline residue: H 98 - end of helix removed outlier: 3.817A pdb=" N GLN H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE H 120 " --> pdb=" O ALA H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 137 removed outlier: 3.887A pdb=" N GLY H 131 " --> pdb=" O HIS H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 156 removed outlier: 4.187A pdb=" N ALA H 142 " --> pdb=" O VAL H 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 8 Processing helix chain 'I' and resid 11 through 46 removed outlier: 3.707A pdb=" N SER I 26 " --> pdb=" O ALA I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 50 No H-bonds generated for 'chain 'I' and resid 48 through 50' Processing helix chain 'I' and resid 51 through 61 Processing helix chain 'I' and resid 63 through 79 removed outlier: 4.020A pdb=" N LEU I 67 " --> pdb=" O GLY I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 124 Proline residue: I 98 - end of helix removed outlier: 3.741A pdb=" N GLN I 119 " --> pdb=" O ALA I 115 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE I 120 " --> pdb=" O ALA I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 137 removed outlier: 4.214A pdb=" N GLY I 131 " --> pdb=" O HIS I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 156 removed outlier: 4.108A pdb=" N ALA I 142 " --> pdb=" O VAL I 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 8 Processing helix chain 'J' and resid 11 through 46 removed outlier: 3.584A pdb=" N SER J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 50 No H-bonds generated for 'chain 'J' and resid 48 through 50' Processing helix chain 'J' and resid 51 through 61 Processing helix chain 'J' and resid 63 through 78 removed outlier: 3.815A pdb=" N LEU J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 124 removed outlier: 3.587A pdb=" N LEU J 97 " --> pdb=" O LEU J 93 " (cutoff:3.500A) Proline residue: J 98 - end of helix removed outlier: 3.857A pdb=" N GLN J 119 " --> pdb=" O ALA J 115 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE J 120 " --> pdb=" O ALA J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 137 removed outlier: 3.967A pdb=" N GLY J 131 " --> pdb=" O HIS J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 156 removed outlier: 4.169A pdb=" N ALA J 142 " --> pdb=" O VAL J 138 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 29 removed outlier: 4.681A pdb=" N GLN P 23 " --> pdb=" O GLU P 19 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N HIS P 29 " --> pdb=" O VAL P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 48 removed outlier: 4.386A pdb=" N VAL P 46 " --> pdb=" O ASN P 42 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU P 47 " --> pdb=" O ASN P 43 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR P 48 " --> pdb=" O GLN P 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 42 through 48' Processing helix chain 'P' and resid 271 through 281 removed outlier: 4.041A pdb=" N GLU P 278 " --> pdb=" O LEU P 274 " (cutoff:3.500A) Processing helix chain 'P' and resid 304 through 315 Processing helix chain 'P' and resid 328 through 334 Processing helix chain 'P' and resid 346 through 348 No H-bonds generated for 'chain 'P' and resid 346 through 348' Processing helix chain 'P' and resid 349 through 357 removed outlier: 3.629A pdb=" N THR P 353 " --> pdb=" O PHE P 349 " (cutoff:3.500A) Processing helix chain 'P' and resid 366 through 383 Proline residue: P 372 - end of helix Processing helix chain 'P' and resid 384 through 401 Processing helix chain 'P' and resid 405 through 430 removed outlier: 3.551A pdb=" N ARG P 410 " --> pdb=" O ARG P 406 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE P 411 " --> pdb=" O GLY P 407 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE P 420 " --> pdb=" O GLU P 416 " (cutoff:3.500A) Proline residue: P 421 - end of helix Processing helix chain 'P' and resid 456 through 483 Processing helix chain 'P' and resid 563 through 571 removed outlier: 3.949A pdb=" N TYR P 571 " --> pdb=" O ASP P 567 " (cutoff:3.500A) Processing helix chain 'P' and resid 572 through 593 Processing helix chain 'P' and resid 596 through 601 removed outlier: 3.743A pdb=" N PHE P 601 " --> pdb=" O PRO P 597 " (cutoff:3.500A) Processing helix chain 'P' and resid 603 through 635 Processing helix chain 'P' and resid 635 through 640 removed outlier: 4.006A pdb=" N PHE P 639 " --> pdb=" O PHE P 635 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 31 through 33 1211 hydrogen bonds defined for protein. 3620 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: 3.03 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2414 1.32 - 1.45: 3589 1.45 - 1.57: 8741 1.57 - 1.70: 20 1.70 - 1.82: 170 Bond restraints: 14934 Sorted by residual: bond pdb=" CAJ W3K P 701 " pdb=" CAK W3K P 701 " ideal model delta sigma weight residual 1.458 1.332 0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" CAA W3K P 701 " pdb=" CAB W3K P 701 " ideal model delta sigma weight residual 1.494 1.389 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" CAD W3K P 701 " pdb=" CAH W3K P 701 " ideal model delta sigma weight residual 1.436 1.331 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" CAJ W3K P 701 " pdb=" NAI W3K P 701 " ideal model delta sigma weight residual 1.410 1.321 0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" CAP W3K P 701 " pdb=" NAQ W3K P 701 " ideal model delta sigma weight residual 1.415 1.330 0.085 2.00e-02 2.50e+03 1.81e+01 ... (remaining 14929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 19851 2.57 - 5.13: 323 5.13 - 7.70: 36 7.70 - 10.27: 16 10.27 - 12.84: 4 Bond angle restraints: 20230 Sorted by residual: angle pdb=" C51 CDL I 201 " pdb=" CB5 CDL I 201 " pdb=" OB6 CDL I 201 " ideal model delta sigma weight residual 111.33 124.17 -12.84 1.32e+00 5.72e-01 9.43e+01 angle pdb=" C51 CDL F 202 " pdb=" CB5 CDL F 202 " pdb=" OB6 CDL F 202 " ideal model delta sigma weight residual 111.33 123.37 -12.04 1.32e+00 5.72e-01 8.29e+01 angle pdb=" C51 CDL H 201 " pdb=" CB5 CDL H 201 " pdb=" OB6 CDL H 201 " ideal model delta sigma weight residual 111.33 122.27 -10.94 1.32e+00 5.72e-01 6.84e+01 angle pdb=" OB6 CDL I 201 " pdb=" CB5 CDL I 201 " pdb=" OB7 CDL I 201 " ideal model delta sigma weight residual 123.92 117.39 6.53 1.00e+00 9.92e-01 4.23e+01 angle pdb=" OB6 CDL F 202 " pdb=" CB5 CDL F 202 " pdb=" OB7 CDL F 202 " ideal model delta sigma weight residual 123.92 117.58 6.34 1.00e+00 9.92e-01 3.99e+01 ... (remaining 20225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.78: 8206 26.78 - 53.55: 565 53.55 - 80.33: 105 80.33 - 107.11: 16 107.11 - 133.89: 4 Dihedral angle restraints: 8896 sinusoidal: 3425 harmonic: 5471 Sorted by residual: dihedral pdb=" CA5 CDL I 201 " pdb=" CA4 CDL I 201 " pdb=" OA6 CDL I 201 " pdb=" CA6 CDL I 201 " ideal model delta sinusoidal sigma weight residual 168.24 -57.87 -133.89 1 3.00e+01 1.11e-03 1.81e+01 dihedral pdb=" CA5 CDL H 201 " pdb=" CA4 CDL H 201 " pdb=" OA6 CDL H 201 " pdb=" CA6 CDL H 201 " ideal model delta sinusoidal sigma weight residual 168.24 -65.97 -125.79 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" CA5 CDL A 201 " pdb=" CA4 CDL A 201 " pdb=" OA6 CDL A 201 " pdb=" CA6 CDL A 201 " ideal model delta sinusoidal sigma weight residual 168.24 -68.75 -123.01 1 3.00e+01 1.11e-03 1.65e+01 ... (remaining 8893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 2405 0.143 - 0.286: 13 0.286 - 0.429: 3 0.429 - 0.572: 1 0.572 - 0.715: 3 Chirality restraints: 2425 Sorted by residual: chirality pdb=" CB4 CDL I 201 " pdb=" CB3 CDL I 201 " pdb=" CB6 CDL I 201 " pdb=" OB6 CDL I 201 " both_signs ideal model delta sigma weight residual False -2.57 -1.86 -0.71 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" CB4 CDL H 201 " pdb=" CB3 CDL H 201 " pdb=" CB6 CDL H 201 " pdb=" OB6 CDL H 201 " both_signs ideal model delta sigma weight residual False -2.57 -1.89 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CB4 CDL F 202 " pdb=" CB3 CDL F 202 " pdb=" CB6 CDL F 202 " pdb=" OB6 CDL F 202 " both_signs ideal model delta sigma weight residual False -2.57 -1.96 -0.61 2.00e-01 2.50e+01 9.35e+00 ... (remaining 2422 not shown) Planarity restraints: 2493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.054 2.00e-02 2.50e+03 2.94e-02 1.73e+01 pdb=" CG TYR A 141 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 141 " -0.050 2.00e-02 2.50e+03 2.70e-02 1.46e+01 pdb=" CG TYR B 141 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR B 141 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 141 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 141 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 141 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 141 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 141 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 141 " 0.047 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" CG TYR G 141 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR G 141 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR G 141 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR G 141 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR G 141 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR G 141 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR G 141 " 0.015 2.00e-02 2.50e+03 ... (remaining 2490 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1372 2.73 - 3.27: 16317 3.27 - 3.82: 27716 3.82 - 4.36: 34347 4.36 - 4.90: 56078 Nonbonded interactions: 135830 Sorted by model distance: nonbonded pdb=" O HOH E 317 " pdb=" O HOH E 321 " model vdw 2.191 3.040 nonbonded pdb=" O HOH C 215 " pdb=" O HOH C 217 " model vdw 2.201 3.040 nonbonded pdb=" O ALA I 43 " pdb=" OG1 THR I 46 " model vdw 2.201 3.040 nonbonded pdb=" O HOH E 319 " pdb=" O HOH E 321 " model vdw 2.203 3.040 nonbonded pdb=" O GLY F 117 " pdb=" O HOH F 301 " model vdw 2.210 3.040 ... (remaining 135825 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 12 or resid 14 through 16 or resid 18 or resid 2 \ 0 or resid 22 through 53 or resid 55 through 56 or resid 58 through 66 or resid \ 68 through 74 or resid 76 through 118 or resid 120 through 156)) selection = (chain 'B' and (resid 1 through 12 or resid 14 through 16 or resid 18 or resid 2 \ 0 or resid 22 through 53 or resid 55 through 56 or resid 58 through 66 or resid \ 68 through 74 or resid 76 through 118 or resid 120 through 156)) selection = (chain 'C' and (resid 1 through 12 or resid 14 through 16 or resid 18 or resid 2 \ 0 or resid 22 through 53 or resid 55 through 56 or resid 58 through 66 or resid \ 68 through 74 or resid 76 through 118 or resid 120 through 156)) selection = (chain 'D' and (resid 1 through 12 or resid 14 through 16 or resid 18 or resid 2 \ 0 or resid 22 through 53 or resid 55 through 56 or resid 58 through 66 or resid \ 68 through 74 or resid 76 through 118 or resid 120 through 156)) selection = (chain 'E' and (resid 1 through 12 or resid 14 through 16 or resid 18 or resid 2 \ 0 or resid 22 through 53 or resid 55 through 56 or resid 58 through 66 or resid \ 68 through 74 or resid 76 through 118 or resid 120 through 156)) selection = (chain 'F' and (resid 1 through 12 or resid 14 through 16 or resid 18 or resid 2 \ 0 or resid 22 through 53 or resid 55 through 56 or resid 58 through 66 or resid \ 68 through 74 or resid 76 through 118 or resid 120 through 156)) selection = (chain 'G' and (resid 1 through 12 or resid 14 through 16 or resid 18 or resid 2 \ 0 or resid 22 through 53 or resid 55 through 56 or resid 58 through 66 or resid \ 68 through 74 or resid 76 through 118 or resid 120 through 156)) selection = (chain 'H' and (resid 1 through 12 or resid 14 through 16 or resid 18 or resid 2 \ 0 or resid 22 through 53 or resid 55 through 56 or resid 58 through 66 or resid \ 68 through 74 or resid 76 through 118 or resid 120 through 156)) selection = (chain 'I' and (resid 1 through 12 or resid 14 through 16 or resid 18 or resid 2 \ 0 or resid 22 through 53 or resid 55 through 56 or resid 58 through 66 or resid \ 68 through 74 or resid 76 through 118 or resid 120 through 156)) selection = (chain 'J' and (resid 1 through 12 or resid 14 through 16 or resid 18 or resid 2 \ 0 or resid 22 through 53 or resid 55 through 56 or resid 58 through 66 or resid \ 68 through 74 or resid 76 through 118 or resid 120 through 156)) } 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=0.50 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.010 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 0.008 0.126 14934 Z= 0.360 Angle : 0.861 12.837 20230 Z= 0.476 Chirality : 0.058 0.715 2425 Planarity : 0.005 0.038 2493 Dihedral : 18.724 133.886 5444 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.62 % Allowed : 17.11 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.18), residues: 1944 helix: 1.22 (0.12), residues: 1645 sheet: 1.62 (1.19), residues: 22 loop : -1.17 (0.32), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 279 TYR 0.057 0.006 TYR A 141 PHE 0.040 0.004 PHE B 101 TRP 0.007 0.002 TRP P 425 HIS 0.007 0.002 HIS H 127 Details of bonding type rmsd covalent geometry : bond 0.00785 (14934) covalent geometry : angle 0.86079 (20230) hydrogen bonds : bond 0.09984 ( 1211) hydrogen bonds : angle 5.42196 ( 3620) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 209 time to evaluate : 0.532 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 213 average time/residue: 0.8337 time to fit residues: 190.6725 Evaluate side-chains 206 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 201 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 323 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 GLN I 88 GLN P 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.094387 restraints weight = 99798.590| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.59 r_work: 0.2939 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14934 Z= 0.147 Angle : 0.551 8.267 20230 Z= 0.302 Chirality : 0.039 0.206 2425 Planarity : 0.003 0.033 2493 Dihedral : 14.403 144.466 2425 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.51 % Allowed : 16.15 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.18), residues: 1944 helix: 1.97 (0.12), residues: 1635 sheet: 1.84 (1.14), residues: 22 loop : -1.38 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 18 TYR 0.036 0.003 TYR A 141 PHE 0.020 0.001 PHE C 101 TRP 0.003 0.001 TRP P 425 HIS 0.004 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00272 (14934) covalent geometry : angle 0.55082 (20230) hydrogen bonds : bond 0.05869 ( 1211) hydrogen bonds : angle 4.71210 ( 3620) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 232 time to evaluate : 0.527 Fit side-chains REVERT: B 12 MET cc_start: 0.8293 (tpp) cc_final: 0.7975 (tpp) REVERT: P 5 LYS cc_start: 0.7262 (mtmt) cc_final: 0.6919 (mmmt) REVERT: P 39 GLU cc_start: 0.5443 (pm20) cc_final: 0.4807 (pp20) REVERT: P 606 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7194 (tp) outliers start: 20 outliers final: 8 residues processed: 243 average time/residue: 0.7545 time to fit residues: 198.4995 Evaluate side-chains 225 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 216 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 23 GLN Chi-restraints excluded: chain P residue 305 GLN Chi-restraints excluded: chain P residue 606 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 81 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 140 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 GLN C 48 GLN D 88 GLN F 88 GLN G 8 GLN I 88 GLN P 296 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.130321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.092511 restraints weight = 96556.176| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.58 r_work: 0.2907 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14934 Z= 0.157 Angle : 0.566 9.087 20230 Z= 0.309 Chirality : 0.040 0.179 2425 Planarity : 0.004 0.035 2493 Dihedral : 13.873 145.969 2422 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.72 % Allowed : 16.29 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.18), residues: 1944 helix: 1.98 (0.12), residues: 1656 sheet: 2.05 (1.11), residues: 22 loop : -0.96 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG P 18 TYR 0.038 0.003 TYR A 141 PHE 0.023 0.002 PHE C 101 TRP 0.003 0.001 TRP P 425 HIS 0.004 0.001 HIS H 127 Details of bonding type rmsd covalent geometry : bond 0.00302 (14934) covalent geometry : angle 0.56555 (20230) hydrogen bonds : bond 0.06277 ( 1211) hydrogen bonds : angle 4.73415 ( 3620) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.488 Fit side-chains REVERT: B 12 MET cc_start: 0.8319 (tpp) cc_final: 0.7988 (tpp) REVERT: B 124 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8234 (mmmt) REVERT: E 1 MET cc_start: 0.6978 (tpp) cc_final: 0.6605 (tpp) REVERT: J 19 MET cc_start: 0.8946 (mtm) cc_final: 0.8742 (mtp) REVERT: P 5 LYS cc_start: 0.7192 (mtmt) cc_final: 0.6879 (mmmt) REVERT: P 39 GLU cc_start: 0.5471 (OUTLIER) cc_final: 0.5113 (tm-30) outliers start: 23 outliers final: 9 residues processed: 230 average time/residue: 0.7683 time to fit residues: 190.5355 Evaluate side-chains 225 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 214 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 305 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 GLN D 88 GLN F 88 GLN G 8 GLN I 88 GLN P 296 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.131174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.093487 restraints weight = 99553.173| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.60 r_work: 0.2923 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14934 Z= 0.148 Angle : 0.544 8.920 20230 Z= 0.298 Chirality : 0.039 0.149 2425 Planarity : 0.003 0.034 2493 Dihedral : 13.385 144.948 2419 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.72 % Allowed : 16.56 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.18), residues: 1944 helix: 2.11 (0.12), residues: 1636 sheet: 2.33 (1.13), residues: 22 loop : -1.21 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 34 TYR 0.036 0.003 TYR A 141 PHE 0.019 0.002 PHE C 101 TRP 0.003 0.001 TRP P 425 HIS 0.003 0.001 HIS H 127 Details of bonding type rmsd covalent geometry : bond 0.00281 (14934) covalent geometry : angle 0.54431 (20230) hydrogen bonds : bond 0.06020 ( 1211) hydrogen bonds : angle 4.65587 ( 3620) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.542 Fit side-chains REVERT: A 12 MET cc_start: 0.8525 (tpp) cc_final: 0.8222 (tpp) REVERT: B 12 MET cc_start: 0.8313 (tpp) cc_final: 0.8011 (tpp) REVERT: B 124 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8190 (mmmt) REVERT: E 1 MET cc_start: 0.6823 (tpp) cc_final: 0.6367 (tpp) REVERT: P 5 LYS cc_start: 0.7190 (mtmt) cc_final: 0.6882 (mmmt) REVERT: P 39 GLU cc_start: 0.5484 (OUTLIER) cc_final: 0.5127 (tm-30) outliers start: 23 outliers final: 10 residues processed: 235 average time/residue: 0.7561 time to fit residues: 191.9658 Evaluate side-chains 223 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 211 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain P residue 23 GLN Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 305 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 170 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 GLN D 88 GLN F 88 GLN P 296 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.128287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.090436 restraints weight = 88903.698| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.48 r_work: 0.2873 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14934 Z= 0.190 Angle : 0.618 9.507 20230 Z= 0.338 Chirality : 0.042 0.173 2425 Planarity : 0.004 0.031 2493 Dihedral : 13.439 147.750 2417 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.06 % Allowed : 15.88 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.18), residues: 1944 helix: 1.87 (0.12), residues: 1656 sheet: 2.21 (1.12), residues: 22 loop : -0.88 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG P 18 TYR 0.045 0.004 TYR A 141 PHE 0.030 0.002 PHE B 101 TRP 0.004 0.001 TRP P 425 HIS 0.004 0.001 HIS H 127 Details of bonding type rmsd covalent geometry : bond 0.00393 (14934) covalent geometry : angle 0.61834 (20230) hydrogen bonds : bond 0.06975 ( 1211) hydrogen bonds : angle 4.89023 ( 3620) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.581 Fit side-chains REVERT: A 12 MET cc_start: 0.8667 (tpp) cc_final: 0.8398 (tpp) REVERT: B 124 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8311 (mmmt) REVERT: E 1 MET cc_start: 0.6841 (tpp) cc_final: 0.6338 (tpp) REVERT: P 5 LYS cc_start: 0.7262 (mtmt) cc_final: 0.6942 (mmmt) REVERT: P 19 GLU cc_start: 0.5305 (mm-30) cc_final: 0.4858 (mp0) REVERT: P 39 GLU cc_start: 0.5453 (OUTLIER) cc_final: 0.5147 (tp30) REVERT: P 313 ASN cc_start: 0.5057 (OUTLIER) cc_final: 0.4679 (m-40) outliers start: 27 outliers final: 13 residues processed: 231 average time/residue: 0.7512 time to fit residues: 187.6203 Evaluate side-chains 228 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain P residue 23 GLN Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 313 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 125 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 GLN D 88 GLN F 88 GLN G 8 GLN I 88 GLN J 155 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.093708 restraints weight = 92769.778| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.53 r_work: 0.2927 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14934 Z= 0.149 Angle : 0.549 9.799 20230 Z= 0.299 Chirality : 0.039 0.146 2425 Planarity : 0.003 0.033 2493 Dihedral : 13.041 149.320 2417 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.65 % Allowed : 16.22 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.18), residues: 1944 helix: 2.05 (0.12), residues: 1659 sheet: 2.15 (1.12), residues: 22 loop : -1.03 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 34 TYR 0.037 0.003 TYR I 141 PHE 0.018 0.002 PHE E 101 TRP 0.003 0.001 TRP P 425 HIS 0.002 0.001 HIS H 127 Details of bonding type rmsd covalent geometry : bond 0.00282 (14934) covalent geometry : angle 0.54872 (20230) hydrogen bonds : bond 0.05986 ( 1211) hydrogen bonds : angle 4.64852 ( 3620) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 220 time to evaluate : 0.458 Fit side-chains REVERT: A 12 MET cc_start: 0.8570 (tpp) cc_final: 0.8273 (tpp) REVERT: B 124 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8239 (mmmt) REVERT: E 1 MET cc_start: 0.6789 (tpp) cc_final: 0.6387 (tpp) REVERT: P 5 LYS cc_start: 0.7243 (mtmt) cc_final: 0.6874 (mmmt) REVERT: P 19 GLU cc_start: 0.5334 (mm-30) cc_final: 0.5042 (tp30) REVERT: P 39 GLU cc_start: 0.5440 (OUTLIER) cc_final: 0.5089 (tm-30) outliers start: 21 outliers final: 10 residues processed: 230 average time/residue: 0.7554 time to fit residues: 188.2420 Evaluate side-chains 223 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 211 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 23 GLN Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 305 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 161 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 GLN D 88 GLN F 88 GLN I 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.130688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.092969 restraints weight = 96521.071| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.56 r_work: 0.2916 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14934 Z= 0.153 Angle : 0.560 9.951 20230 Z= 0.305 Chirality : 0.039 0.146 2425 Planarity : 0.003 0.032 2493 Dihedral : 12.883 149.742 2417 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.51 % Allowed : 16.98 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.18), residues: 1944 helix: 2.05 (0.12), residues: 1658 sheet: 2.16 (1.14), residues: 22 loop : -1.01 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 279 TYR 0.038 0.003 TYR E 141 PHE 0.021 0.002 PHE B 101 TRP 0.003 0.001 TRP P 425 HIS 0.003 0.001 HIS H 127 Details of bonding type rmsd covalent geometry : bond 0.00294 (14934) covalent geometry : angle 0.55988 (20230) hydrogen bonds : bond 0.06146 ( 1211) hydrogen bonds : angle 4.67784 ( 3620) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 216 time to evaluate : 0.469 Fit side-chains REVERT: A 12 MET cc_start: 0.8594 (tpp) cc_final: 0.8325 (tpp) REVERT: B 124 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8239 (mmmt) REVERT: E 1 MET cc_start: 0.6862 (tpp) cc_final: 0.6452 (tpp) REVERT: P 5 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6875 (mmmt) REVERT: P 39 GLU cc_start: 0.5454 (OUTLIER) cc_final: 0.5105 (tm-30) outliers start: 19 outliers final: 11 residues processed: 229 average time/residue: 0.7633 time to fit residues: 188.9840 Evaluate side-chains 223 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 299 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 147 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 141 optimal weight: 0.2980 chunk 171 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 GLN D 88 GLN F 88 GLN I 88 GLN J 155 ASN P 296 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.130920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.093337 restraints weight = 95343.735| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.56 r_work: 0.2927 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14934 Z= 0.152 Angle : 0.559 10.391 20230 Z= 0.304 Chirality : 0.039 0.140 2425 Planarity : 0.003 0.032 2493 Dihedral : 12.749 149.547 2417 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.44 % Allowed : 17.18 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.18), residues: 1944 helix: 2.07 (0.12), residues: 1658 sheet: 2.10 (1.13), residues: 22 loop : -1.02 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 279 TYR 0.040 0.003 TYR E 141 PHE 0.020 0.002 PHE B 101 TRP 0.003 0.001 TRP P 425 HIS 0.002 0.001 HIS H 127 Details of bonding type rmsd covalent geometry : bond 0.00291 (14934) covalent geometry : angle 0.55864 (20230) hydrogen bonds : bond 0.06087 ( 1211) hydrogen bonds : angle 4.66238 ( 3620) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 0.517 Fit side-chains REVERT: A 12 MET cc_start: 0.8606 (tpp) cc_final: 0.8348 (tpp) REVERT: B 124 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8199 (mmmt) REVERT: E 1 MET cc_start: 0.6841 (tpp) cc_final: 0.6362 (tpp) REVERT: P 5 LYS cc_start: 0.7254 (mtmt) cc_final: 0.6887 (mmmt) REVERT: P 19 GLU cc_start: 0.5330 (mm-30) cc_final: 0.5044 (tp30) REVERT: P 39 GLU cc_start: 0.5440 (OUTLIER) cc_final: 0.5054 (tm-30) outliers start: 18 outliers final: 12 residues processed: 227 average time/residue: 0.7686 time to fit residues: 188.7502 Evaluate side-chains 225 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 211 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 305 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 127 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 126 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 GLN D 88 GLN F 88 GLN I 88 GLN P 296 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.131492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.094070 restraints weight = 91685.758| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.52 r_work: 0.2944 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14934 Z= 0.147 Angle : 0.557 10.645 20230 Z= 0.302 Chirality : 0.039 0.134 2425 Planarity : 0.003 0.034 2493 Dihedral : 12.589 149.755 2417 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.24 % Allowed : 17.59 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.18), residues: 1944 helix: 2.10 (0.12), residues: 1658 sheet: 2.23 (1.16), residues: 22 loop : -1.03 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG P 279 TYR 0.040 0.003 TYR E 141 PHE 0.018 0.002 PHE E 101 TRP 0.003 0.001 TRP P 425 HIS 0.002 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00280 (14934) covalent geometry : angle 0.55731 (20230) hydrogen bonds : bond 0.05905 ( 1211) hydrogen bonds : angle 4.61279 ( 3620) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 217 time to evaluate : 0.474 Fit side-chains REVERT: A 12 MET cc_start: 0.8596 (tpp) cc_final: 0.8342 (tpp) REVERT: B 124 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8208 (mmmt) REVERT: E 1 MET cc_start: 0.6737 (tpp) cc_final: 0.6346 (tpp) REVERT: P 5 LYS cc_start: 0.7196 (mtmt) cc_final: 0.6851 (mmmt) REVERT: P 19 GLU cc_start: 0.5282 (mm-30) cc_final: 0.5009 (tp30) REVERT: P 39 GLU cc_start: 0.5440 (OUTLIER) cc_final: 0.5052 (tm-30) outliers start: 15 outliers final: 13 residues processed: 227 average time/residue: 0.7796 time to fit residues: 190.9801 Evaluate side-chains 223 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 305 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 150 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 GLN D 88 GLN F 88 GLN I 88 GLN J 155 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.129385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.091638 restraints weight = 83996.779| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.44 r_work: 0.2897 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14934 Z= 0.176 Angle : 0.612 10.959 20230 Z= 0.331 Chirality : 0.041 0.158 2425 Planarity : 0.004 0.032 2493 Dihedral : 12.779 149.994 2417 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.31 % Allowed : 17.73 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.18), residues: 1944 helix: 1.95 (0.12), residues: 1658 sheet: 2.20 (1.14), residues: 22 loop : -1.00 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 279 TYR 0.048 0.004 TYR E 141 PHE 0.026 0.002 PHE B 101 TRP 0.004 0.001 TRP P 425 HIS 0.003 0.001 HIS P 626 Details of bonding type rmsd covalent geometry : bond 0.00355 (14934) covalent geometry : angle 0.61154 (20230) hydrogen bonds : bond 0.06631 ( 1211) hydrogen bonds : angle 4.78979 ( 3620) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 0.471 Fit side-chains REVERT: A 12 MET cc_start: 0.8659 (tpp) cc_final: 0.8402 (tpp) REVERT: B 124 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8316 (mmmt) REVERT: E 1 MET cc_start: 0.6783 (tpp) cc_final: 0.6385 (tpp) REVERT: P 5 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6921 (mmmt) REVERT: P 19 GLU cc_start: 0.5314 (mm-30) cc_final: 0.5016 (tp30) REVERT: P 39 GLU cc_start: 0.5435 (OUTLIER) cc_final: 0.5043 (tm-30) REVERT: P 645 ARG cc_start: 0.7631 (mtm-85) cc_final: 0.7299 (mtm-85) outliers start: 16 outliers final: 14 residues processed: 220 average time/residue: 0.7829 time to fit residues: 185.8979 Evaluate side-chains 225 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 305 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 53 optimal weight: 0.9990 chunk 182 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 72 optimal weight: 0.0570 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 GLN D 88 GLN F 88 GLN I 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.094491 restraints weight = 102480.885| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.61 r_work: 0.2940 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14934 Z= 0.146 Angle : 0.561 10.730 20230 Z= 0.301 Chirality : 0.039 0.130 2425 Planarity : 0.003 0.035 2493 Dihedral : 12.513 149.696 2417 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.24 % Allowed : 17.80 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.19), residues: 1944 helix: 2.16 (0.12), residues: 1638 sheet: 2.15 (1.15), residues: 22 loop : -1.32 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 279 TYR 0.039 0.003 TYR E 141 PHE 0.016 0.001 PHE E 101 TRP 0.002 0.001 TRP P 425 HIS 0.003 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00277 (14934) covalent geometry : angle 0.56110 (20230) hydrogen bonds : bond 0.05794 ( 1211) hydrogen bonds : angle 4.59778 ( 3620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8932.00 seconds wall clock time: 152 minutes 9.97 seconds (9129.97 seconds total)