Starting phenix.real_space_refine on Fri Mar 15 17:42:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukh_26581/03_2024/7ukh_26581.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukh_26581/03_2024/7ukh_26581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukh_26581/03_2024/7ukh_26581.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukh_26581/03_2024/7ukh_26581.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukh_26581/03_2024/7ukh_26581.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukh_26581/03_2024/7ukh_26581.pdb" } resolution = 2.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.071 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 Ca 12 9.91 5 Zn 4 6.06 5 S 68 5.16 5 C 7800 2.51 5 N 2116 2.21 5 O 2340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C GLU 486": "OE1" <-> "OE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D GLU 486": "OE1" <-> "OE2" Residue "I GLU 73": "OE1" <-> "OE2" Residue "I GLU 108": "OE1" <-> "OE2" Residue "I GLU 209": "OE1" <-> "OE2" Residue "I GLU 229": "OE1" <-> "OE2" Residue "I GLU 233": "OE1" <-> "OE2" Residue "I GLU 239": "OE1" <-> "OE2" Residue "J GLU 73": "OE1" <-> "OE2" Residue "J GLU 108": "OE1" <-> "OE2" Residue "J GLU 209": "OE1" <-> "OE2" Residue "J GLU 229": "OE1" <-> "OE2" Residue "J GLU 233": "OE1" <-> "OE2" Residue "J GLU 239": "OE1" <-> "OE2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "K GLU 209": "OE1" <-> "OE2" Residue "K GLU 229": "OE1" <-> "OE2" Residue "K GLU 233": "OE1" <-> "OE2" Residue "K GLU 239": "OE1" <-> "OE2" Residue "L GLU 73": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "L GLU 209": "OE1" <-> "OE2" Residue "L GLU 229": "OE1" <-> "OE2" Residue "L GLU 233": "OE1" <-> "OE2" Residue "L GLU 239": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12340 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1612 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 11, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1612 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 11, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1612 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 11, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1612 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 11, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 47 Chain: "I" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1469 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 176} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "J" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1469 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 176} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "K" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1469 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 176} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "L" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1469 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 176} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1019 SG CYS A 132 81.658 84.010 41.310 1.00 20.30 S ATOM 1025 SG CYS A 133 80.730 80.238 41.398 1.00 17.59 S ATOM 2469 SG CYS B 111 78.021 82.956 40.948 1.00 12.57 S ATOM 2631 SG CYS B 132 57.972 81.655 41.247 1.00 20.48 S ATOM 2637 SG CYS B 133 61.741 80.718 41.344 1.00 17.30 S ATOM 4081 SG CYS C 111 59.100 78.039 40.955 1.00 12.64 S ATOM 4243 SG CYS C 132 60.455 57.993 41.243 1.00 20.17 S ATOM 4249 SG CYS C 133 61.381 61.765 41.343 1.00 17.07 S ATOM 5693 SG CYS D 111 64.034 59.105 40.956 1.00 12.92 S ATOM 857 SG CYS A 111 83.004 63.964 40.961 1.00 12.99 S ATOM 5855 SG CYS D 132 84.080 60.459 41.241 1.00 20.54 S ATOM 5861 SG CYS D 133 80.308 61.385 41.342 1.00 17.48 S Time building chain proxies: 6.82, per 1000 atoms: 0.55 Number of scatterers: 12340 At special positions: 0 Unit cell: (142.898, 142.898, 62.776, 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) Zn 4 29.99 Ca 12 19.99 S 68 16.00 O 2340 8.00 N 2116 7.00 C 7800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.37 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" ND1 HIS A 105 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 133 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 132 " pdb="ZN ZN A 901 " - pdb=" SG CYS B 111 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" ND1 HIS B 105 " pdb="ZN ZN B 901 " - pdb=" SG CYS B 133 " pdb="ZN ZN B 901 " - pdb=" SG CYS B 132 " pdb="ZN ZN B 901 " - pdb=" SG CYS C 111 " pdb=" ZN C 901 " pdb="ZN ZN C 901 " - pdb=" ND1 HIS C 105 " pdb="ZN ZN C 901 " - pdb=" SG CYS D 111 " pdb="ZN ZN C 901 " - pdb=" SG CYS C 133 " pdb="ZN ZN C 901 " - pdb=" SG CYS C 132 " pdb=" ZN D 901 " pdb="ZN ZN D 901 " - pdb=" ND1 HIS D 105 " pdb="ZN ZN D 901 " - pdb=" SG CYS A 111 " pdb="ZN ZN D 901 " - pdb=" SG CYS D 133 " pdb="ZN ZN D 901 " - pdb=" SG CYS D 132 " Number of angles added : 12 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2912 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 68.5% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 Processing helix chain 'A' and resid 17 through 19 No H-bonds generated for 'chain 'A' and resid 17 through 19' Processing helix chain 'A' and resid 35 through 39 removed outlier: 3.752A pdb=" N GLN A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.501A pdb=" N LEU A 59 " --> pdb=" O TRP A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 88 through 102 removed outlier: 4.007A pdb=" N HIS A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 130 through 153 removed outlier: 4.603A pdb=" N GLU A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N GLU A 136 " --> pdb=" O CYS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 451 Processing helix chain 'A' and resid 473 through 490 Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'B' and resid 17 through 19 No H-bonds generated for 'chain 'B' and resid 17 through 19' Processing helix chain 'B' and resid 35 through 39 removed outlier: 3.751A pdb=" N GLN B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.501A pdb=" N LEU B 59 " --> pdb=" O TRP B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 88 through 102 removed outlier: 4.007A pdb=" N HIS B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 130 through 153 removed outlier: 4.603A pdb=" N GLU B 135 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N GLU B 136 " --> pdb=" O CYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 451 Processing helix chain 'B' and resid 473 through 490 Processing helix chain 'C' and resid 8 through 16 Processing helix chain 'C' and resid 17 through 19 No H-bonds generated for 'chain 'C' and resid 17 through 19' Processing helix chain 'C' and resid 35 through 39 removed outlier: 3.751A pdb=" N GLN C 39 " --> pdb=" O LYS C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.501A pdb=" N LEU C 59 " --> pdb=" O TRP C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'C' and resid 88 through 102 removed outlier: 4.007A pdb=" N HIS C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 130 through 153 removed outlier: 4.603A pdb=" N GLU C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLU C 136 " --> pdb=" O CYS C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 451 Processing helix chain 'C' and resid 473 through 490 Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 17 through 19 No H-bonds generated for 'chain 'D' and resid 17 through 19' Processing helix chain 'D' and resid 35 through 39 removed outlier: 3.752A pdb=" N GLN D 39 " --> pdb=" O LYS D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 69 through 74 Processing helix chain 'D' and resid 88 through 102 removed outlier: 4.007A pdb=" N HIS D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 122 Processing helix chain 'D' and resid 125 through 129 Processing helix chain 'D' and resid 130 through 153 removed outlier: 4.603A pdb=" N GLU D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLU D 136 " --> pdb=" O CYS D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 451 Processing helix chain 'D' and resid 473 through 490 Processing helix chain 'I' and resid 74 through 82 Processing helix chain 'I' and resid 85 through 100 Processing helix chain 'I' and resid 107 through 116 removed outlier: 3.973A pdb=" N GLN I 116 " --> pdb=" O GLN I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 135 Processing helix chain 'I' and resid 144 through 157 Processing helix chain 'I' and resid 158 through 171 Processing helix chain 'I' and resid 179 through 195 removed outlier: 3.762A pdb=" N MET I 193 " --> pdb=" O SER I 189 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET I 194 " --> pdb=" O ILE I 190 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY I 195 " --> pdb=" O TYR I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 219 Processing helix chain 'I' and resid 228 through 237 Processing helix chain 'I' and resid 238 through 252 removed outlier: 3.631A pdb=" N ASP I 249 " --> pdb=" O MET I 245 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN I 250 " --> pdb=" O GLN I 246 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE I 252 " --> pdb=" O PHE I 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 82 Processing helix chain 'J' and resid 85 through 100 Processing helix chain 'J' and resid 107 through 116 removed outlier: 3.974A pdb=" N GLN J 116 " --> pdb=" O GLN J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 135 Processing helix chain 'J' and resid 144 through 157 Processing helix chain 'J' and resid 158 through 171 Processing helix chain 'J' and resid 179 through 195 removed outlier: 3.762A pdb=" N MET J 193 " --> pdb=" O SER J 189 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET J 194 " --> pdb=" O ILE J 190 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY J 195 " --> pdb=" O TYR J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 219 Processing helix chain 'J' and resid 228 through 237 Processing helix chain 'J' and resid 238 through 252 removed outlier: 3.632A pdb=" N ASP J 249 " --> pdb=" O MET J 245 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN J 250 " --> pdb=" O GLN J 246 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE J 252 " --> pdb=" O PHE J 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 82 Processing helix chain 'K' and resid 85 through 100 Processing helix chain 'K' and resid 107 through 116 removed outlier: 3.973A pdb=" N GLN K 116 " --> pdb=" O GLN K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 135 Processing helix chain 'K' and resid 144 through 157 Processing helix chain 'K' and resid 158 through 171 Processing helix chain 'K' and resid 179 through 195 removed outlier: 3.761A pdb=" N MET K 193 " --> pdb=" O SER K 189 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET K 194 " --> pdb=" O ILE K 190 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY K 195 " --> pdb=" O TYR K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 219 Processing helix chain 'K' and resid 228 through 237 Processing helix chain 'K' and resid 238 through 252 removed outlier: 3.631A pdb=" N ASP K 249 " --> pdb=" O MET K 245 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN K 250 " --> pdb=" O GLN K 246 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE K 252 " --> pdb=" O PHE K 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 82 Processing helix chain 'L' and resid 85 through 100 Processing helix chain 'L' and resid 107 through 116 removed outlier: 3.974A pdb=" N GLN L 116 " --> pdb=" O GLN L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 135 Processing helix chain 'L' and resid 144 through 157 Processing helix chain 'L' and resid 158 through 171 Processing helix chain 'L' and resid 179 through 195 removed outlier: 3.761A pdb=" N MET L 193 " --> pdb=" O SER L 189 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET L 194 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY L 195 " --> pdb=" O TYR L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 219 Processing helix chain 'L' and resid 228 through 237 Processing helix chain 'L' and resid 238 through 252 removed outlier: 3.632A pdb=" N ASP L 249 " --> pdb=" O MET L 245 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN L 250 " --> pdb=" O GLN L 246 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE L 252 " --> pdb=" O PHE L 248 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 54 Processing sheet with id=AA2, first strand: chain 'B' and resid 50 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 50 through 54 Processing sheet with id=AA4, first strand: chain 'D' and resid 50 through 54 Processing sheet with id=AA5, first strand: chain 'I' and resid 104 through 106 Processing sheet with id=AA6, first strand: chain 'I' and resid 177 through 178 Processing sheet with id=AA7, first strand: chain 'J' and resid 104 through 106 Processing sheet with id=AA8, first strand: chain 'J' and resid 177 through 178 Processing sheet with id=AA9, first strand: chain 'K' and resid 104 through 106 Processing sheet with id=AB1, first strand: chain 'K' and resid 177 through 178 Processing sheet with id=AB2, first strand: chain 'L' and resid 104 through 106 Processing sheet with id=AB3, first strand: chain 'L' and resid 177 through 178 741 hydrogen bonds defined for protein. 2103 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: 3.52 Time building geometry restraints manager: 5.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4093 1.34 - 1.46: 2000 1.46 - 1.57: 6419 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 12620 Sorted by residual: bond pdb=" N ALA A 145 " pdb=" CA ALA A 145 " ideal model delta sigma weight residual 1.459 1.483 -0.023 1.21e-02 6.83e+03 3.76e+00 bond pdb=" N ALA D 145 " pdb=" CA ALA D 145 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.21e-02 6.83e+03 3.68e+00 bond pdb=" N ALA C 145 " pdb=" CA ALA C 145 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.21e-02 6.83e+03 3.56e+00 bond pdb=" N ALA B 145 " pdb=" CA ALA B 145 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.21e-02 6.83e+03 3.38e+00 bond pdb=" C ASN D 144 " pdb=" N ALA D 145 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.31e-02 5.83e+03 1.83e+00 ... (remaining 12615 not shown) Histogram of bond angle deviations from ideal: 97.40 - 104.72: 189 104.72 - 112.03: 5712 112.03 - 119.35: 4329 119.35 - 126.67: 6663 126.67 - 133.99: 151 Bond angle restraints: 17044 Sorted by residual: angle pdb=" CA TRP C 19 " pdb=" CB TRP C 19 " pdb=" CG TRP C 19 " ideal model delta sigma weight residual 113.60 117.74 -4.14 1.90e+00 2.77e-01 4.74e+00 angle pdb=" CA TRP D 19 " pdb=" CB TRP D 19 " pdb=" CG TRP D 19 " ideal model delta sigma weight residual 113.60 117.71 -4.11 1.90e+00 2.77e-01 4.69e+00 angle pdb=" CA TRP B 19 " pdb=" CB TRP B 19 " pdb=" CG TRP B 19 " ideal model delta sigma weight residual 113.60 117.69 -4.09 1.90e+00 2.77e-01 4.64e+00 angle pdb=" CA TRP A 19 " pdb=" CB TRP A 19 " pdb=" CG TRP A 19 " ideal model delta sigma weight residual 113.60 117.69 -4.09 1.90e+00 2.77e-01 4.64e+00 angle pdb=" O ASN C 144 " pdb=" C ASN C 144 " pdb=" N ALA C 145 " ideal model delta sigma weight residual 122.27 120.04 2.23 1.23e+00 6.61e-01 3.28e+00 ... (remaining 17039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 6518 17.84 - 35.67: 690 35.67 - 53.51: 236 53.51 - 71.35: 52 71.35 - 89.18: 32 Dihedral angle restraints: 7528 sinusoidal: 3032 harmonic: 4496 Sorted by residual: dihedral pdb=" CB GLU K 145 " pdb=" CG GLU K 145 " pdb=" CD GLU K 145 " pdb=" OE1 GLU K 145 " ideal model delta sinusoidal sigma weight residual 0.00 -89.18 89.18 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU I 145 " pdb=" CG GLU I 145 " pdb=" CD GLU I 145 " pdb=" OE1 GLU I 145 " ideal model delta sinusoidal sigma weight residual 0.00 -89.18 89.18 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU J 145 " pdb=" CG GLU J 145 " pdb=" CD GLU J 145 " pdb=" OE1 GLU J 145 " ideal model delta sinusoidal sigma weight residual 0.00 -89.14 89.14 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 7525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 948 0.028 - 0.057: 513 0.057 - 0.085: 182 0.085 - 0.114: 107 0.114 - 0.142: 18 Chirality restraints: 1768 Sorted by residual: chirality pdb=" CG LEU K 163 " pdb=" CB LEU K 163 " pdb=" CD1 LEU K 163 " pdb=" CD2 LEU K 163 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CG LEU L 163 " pdb=" CB LEU L 163 " pdb=" CD1 LEU L 163 " pdb=" CD2 LEU L 163 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CG LEU I 163 " pdb=" CB LEU I 163 " pdb=" CD1 LEU I 163 " pdb=" CD2 LEU I 163 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 1765 not shown) Planarity restraints: 2264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 144 " 0.016 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C ASN C 144 " -0.053 2.00e-02 2.50e+03 pdb=" O ASN C 144 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA C 145 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 144 " 0.016 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C ASN B 144 " -0.053 2.00e-02 2.50e+03 pdb=" O ASN B 144 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA B 145 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 144 " 0.016 2.00e-02 2.50e+03 3.04e-02 9.24e+00 pdb=" C ASN D 144 " -0.053 2.00e-02 2.50e+03 pdb=" O ASN D 144 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA D 145 " 0.018 2.00e-02 2.50e+03 ... (remaining 2261 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 247 2.61 - 3.18: 11232 3.18 - 3.75: 20579 3.75 - 4.33: 29414 4.33 - 4.90: 45684 Nonbonded interactions: 107156 Sorted by model distance: nonbonded pdb=" OD1 ASP J 135 " pdb=" O SER J 141 " model vdw 2.035 3.040 nonbonded pdb=" OD1 ASP I 135 " pdb=" O SER I 141 " model vdw 2.036 3.040 nonbonded pdb=" OD1 ASP K 135 " pdb=" O SER K 141 " model vdw 2.036 3.040 nonbonded pdb=" OD1 ASP L 135 " pdb=" O SER L 141 " model vdw 2.036 3.040 nonbonded pdb=" OD1 ASP K 219 " pdb="CA CA K 903 " model vdw 2.170 2.510 ... (remaining 107151 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.490 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: 24.020 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 37.400 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.090 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:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 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 : 0.004 0.027 12620 Z= 0.279 Angle : 0.609 5.974 17044 Z= 0.350 Chirality : 0.043 0.142 1768 Planarity : 0.004 0.034 2264 Dihedral : 17.880 89.183 4616 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.80 % Allowed : 18.05 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.22), residues: 1504 helix: 1.15 (0.17), residues: 968 sheet: -0.43 (0.86), residues: 40 loop : -0.07 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 19 HIS 0.005 0.001 HIS B 77 PHE 0.018 0.002 PHE D 84 TYR 0.014 0.002 TYR L 126 ARG 0.003 0.001 ARG B 434 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 241 time to evaluate : 1.509 Fit side-chains outliers start: 23 outliers final: 10 residues processed: 258 average time/residue: 1.5135 time to fit residues: 416.2072 Evaluate side-chains 237 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 227 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 234 SER Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 234 SER Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 234 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 477 GLN A 490 ASN B 56 GLN B 477 GLN B 490 ASN C 56 GLN C 477 GLN C 490 ASN D 56 GLN D 477 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12620 Z= 0.292 Angle : 0.575 5.764 17044 Z= 0.311 Chirality : 0.043 0.123 1768 Planarity : 0.005 0.037 2264 Dihedral : 4.725 32.649 1688 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.75 % Allowed : 18.12 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.22), residues: 1504 helix: 1.24 (0.17), residues: 968 sheet: -0.93 (0.81), residues: 40 loop : -0.05 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 19 HIS 0.006 0.001 HIS D 77 PHE 0.020 0.003 PHE A 84 TYR 0.013 0.002 TYR D 444 ARG 0.005 0.001 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 232 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 19 residues processed: 255 average time/residue: 1.6156 time to fit residues: 438.2788 Evaluate side-chains 237 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 218 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 77 GLN Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 232 ILE Chi-restraints excluded: chain J residue 236 GLN Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 236 GLN Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 209 GLU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 232 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 114 optimal weight: 0.0980 chunk 93 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 138 optimal weight: 0.5980 chunk 149 optimal weight: 0.2980 chunk 123 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 477 GLN B 56 GLN B 477 GLN C 56 GLN C 477 GLN D 56 GLN D 477 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12620 Z= 0.160 Angle : 0.473 5.075 17044 Z= 0.254 Chirality : 0.039 0.126 1768 Planarity : 0.003 0.026 2264 Dihedral : 4.313 33.290 1680 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.44 % Allowed : 19.45 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.22), residues: 1504 helix: 1.57 (0.17), residues: 968 sheet: -0.34 (0.87), residues: 40 loop : -0.03 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 19 HIS 0.003 0.001 HIS D 77 PHE 0.013 0.002 PHE A 84 TYR 0.008 0.001 TYR A 115 ARG 0.002 0.000 ARG C 434 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 232 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 ARG cc_start: 0.7280 (mpt180) cc_final: 0.7041 (mtt-85) outliers start: 44 outliers final: 14 residues processed: 250 average time/residue: 1.5491 time to fit residues: 413.2037 Evaluate side-chains 238 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 224 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 236 GLN Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 236 GLN Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 225 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 131 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 477 GLN B 56 GLN B 477 GLN C 56 GLN C 477 GLN D 56 GLN D 477 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12620 Z= 0.270 Angle : 0.536 5.748 17044 Z= 0.287 Chirality : 0.042 0.121 1768 Planarity : 0.004 0.036 2264 Dihedral : 4.417 35.558 1680 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.67 % Allowed : 19.38 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.22), residues: 1504 helix: 1.52 (0.17), residues: 968 sheet: -0.92 (0.81), residues: 40 loop : -0.08 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 19 HIS 0.004 0.001 HIS D 491 PHE 0.019 0.003 PHE L 118 TYR 0.012 0.002 TYR A 106 ARG 0.004 0.001 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 219 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 ARG cc_start: 0.7198 (mpt180) cc_final: 0.6979 (mmt180) REVERT: J 108 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: K 108 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: L 209 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7277 (mp0) outliers start: 47 outliers final: 27 residues processed: 244 average time/residue: 1.6518 time to fit residues: 428.9527 Evaluate side-chains 245 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 215 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 236 GLN Chi-restraints excluded: chain J residue 108 GLU Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 236 GLN Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 236 GLN Chi-restraints excluded: chain L residue 209 GLU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 226 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 0.0770 chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 75 optimal weight: 0.0370 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 477 GLN B 56 GLN B 477 GLN C 56 GLN C 477 GLN D 56 GLN D 477 GLN D 490 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12620 Z= 0.160 Angle : 0.472 5.064 17044 Z= 0.252 Chirality : 0.039 0.124 1768 Planarity : 0.003 0.024 2264 Dihedral : 4.246 35.256 1680 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.81 % Allowed : 19.77 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.22), residues: 1504 helix: 1.68 (0.17), residues: 968 sheet: -0.40 (0.88), residues: 40 loop : -0.02 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 19 HIS 0.003 0.001 HIS A 94 PHE 0.014 0.002 PHE A 84 TYR 0.008 0.001 TYR A 115 ARG 0.002 0.000 ARG A 434 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 233 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 242 MET cc_start: 0.5926 (tpp) cc_final: 0.5280 (tpp) REVERT: J 217 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7664 (tmtt) REVERT: L 209 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7271 (mp0) outliers start: 36 outliers final: 19 residues processed: 247 average time/residue: 1.5896 time to fit residues: 418.0278 Evaluate side-chains 249 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 228 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 236 GLN Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 217 LYS Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 236 GLN Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 236 GLN Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 209 GLU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 236 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 0.0070 chunk 36 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 477 GLN B 56 GLN B 477 GLN C 56 GLN C 477 GLN D 56 GLN D 477 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12620 Z= 0.175 Angle : 0.477 5.049 17044 Z= 0.255 Chirality : 0.039 0.124 1768 Planarity : 0.003 0.025 2264 Dihedral : 4.184 34.998 1680 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.58 % Allowed : 20.00 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.22), residues: 1504 helix: 1.72 (0.17), residues: 968 sheet: -0.31 (0.88), residues: 40 loop : -0.02 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 19 HIS 0.003 0.001 HIS B 77 PHE 0.015 0.002 PHE A 84 TYR 0.008 0.001 TYR B 106 ARG 0.002 0.000 ARG A 434 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 229 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 242 MET cc_start: 0.5861 (tpp) cc_final: 0.5612 (tpp) REVERT: L 209 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7250 (mp0) outliers start: 33 outliers final: 19 residues processed: 241 average time/residue: 1.5949 time to fit residues: 409.9529 Evaluate side-chains 248 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 228 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 236 GLN Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 236 GLN Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 236 GLN Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 209 GLU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 236 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 67 optimal weight: 0.2980 chunk 90 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 477 GLN B 56 GLN B 477 GLN C 56 GLN C 477 GLN D 56 GLN D 477 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12620 Z= 0.190 Angle : 0.489 5.213 17044 Z= 0.260 Chirality : 0.040 0.123 1768 Planarity : 0.003 0.024 2264 Dihedral : 4.199 35.648 1680 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.34 % Allowed : 20.39 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.22), residues: 1504 helix: 1.72 (0.17), residues: 968 sheet: -0.41 (0.87), residues: 40 loop : -0.02 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 19 HIS 0.003 0.001 HIS C 77 PHE 0.015 0.002 PHE A 84 TYR 0.009 0.001 TYR D 106 ARG 0.002 0.000 ARG A 434 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 230 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 242 MET cc_start: 0.5845 (tpp) cc_final: 0.5261 (tpp) REVERT: K 242 MET cc_start: 0.6056 (tpp) cc_final: 0.4920 (tpp) REVERT: L 209 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7236 (mp0) outliers start: 30 outliers final: 21 residues processed: 246 average time/residue: 1.6606 time to fit residues: 435.1363 Evaluate side-chains 251 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 229 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 236 GLN Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 236 GLN Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 236 GLN Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 209 GLU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 236 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 93 optimal weight: 0.0170 chunk 99 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 477 GLN B 56 GLN B 477 GLN C 56 GLN C 477 GLN D 56 GLN D 477 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12620 Z= 0.185 Angle : 0.489 5.346 17044 Z= 0.260 Chirality : 0.040 0.124 1768 Planarity : 0.003 0.025 2264 Dihedral : 4.180 36.039 1680 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.19 % Allowed : 20.94 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.22), residues: 1504 helix: 1.73 (0.17), residues: 968 sheet: -0.36 (0.88), residues: 40 loop : -0.00 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 19 HIS 0.003 0.001 HIS B 94 PHE 0.015 0.002 PHE A 84 TYR 0.009 0.001 TYR A 106 ARG 0.002 0.000 ARG A 434 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 228 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 116 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6991 (mp10) REVERT: I 242 MET cc_start: 0.5931 (tpp) cc_final: 0.5704 (tpp) REVERT: K 108 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: K 242 MET cc_start: 0.6023 (tpp) cc_final: 0.4911 (tpp) REVERT: L 209 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7231 (mp0) outliers start: 28 outliers final: 23 residues processed: 244 average time/residue: 1.6408 time to fit residues: 426.2065 Evaluate side-chains 254 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 228 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain I residue 116 GLN Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 236 GLN Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 236 GLN Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 236 GLN Chi-restraints excluded: chain L residue 116 GLN Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 209 GLU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 236 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 140 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 477 GLN B 56 GLN B 477 GLN C 56 GLN C 477 GLN D 56 GLN D 477 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12620 Z= 0.180 Angle : 0.485 5.455 17044 Z= 0.258 Chirality : 0.039 0.124 1768 Planarity : 0.003 0.025 2264 Dihedral : 4.169 35.940 1680 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.27 % Allowed : 21.25 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.22), residues: 1504 helix: 1.74 (0.17), residues: 968 sheet: -0.31 (0.88), residues: 40 loop : 0.02 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 19 HIS 0.003 0.001 HIS C 94 PHE 0.015 0.002 PHE A 84 TYR 0.008 0.001 TYR A 106 ARG 0.002 0.000 ARG C 434 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 232 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 116 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6952 (mp10) REVERT: I 242 MET cc_start: 0.5858 (tpp) cc_final: 0.5654 (tpp) REVERT: J 242 MET cc_start: 0.5719 (tpp) cc_final: 0.4546 (tpp) REVERT: K 108 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: K 242 MET cc_start: 0.5911 (tpp) cc_final: 0.5194 (tpp) REVERT: L 116 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.7167 (pt0) REVERT: L 209 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: L 242 MET cc_start: 0.5897 (tpp) cc_final: 0.4781 (tpp) outliers start: 29 outliers final: 21 residues processed: 248 average time/residue: 1.6021 time to fit residues: 423.3589 Evaluate side-chains 256 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 231 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain I residue 116 GLN Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 236 GLN Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 236 GLN Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 236 GLN Chi-restraints excluded: chain L residue 116 GLN Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 209 GLU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 236 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 120 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 128 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 477 GLN B 56 GLN B 477 GLN C 56 GLN C 477 GLN D 56 GLN D 477 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12620 Z= 0.174 Angle : 0.490 5.389 17044 Z= 0.260 Chirality : 0.039 0.125 1768 Planarity : 0.003 0.025 2264 Dihedral : 4.143 35.657 1680 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.95 % Allowed : 21.80 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.22), residues: 1504 helix: 1.76 (0.17), residues: 968 sheet: -0.25 (0.89), residues: 40 loop : 0.04 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 19 HIS 0.003 0.001 HIS B 94 PHE 0.015 0.002 PHE A 84 TYR 0.008 0.001 TYR A 106 ARG 0.003 0.000 ARG D 434 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 236 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 116 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6956 (mp10) REVERT: J 242 MET cc_start: 0.5639 (tpp) cc_final: 0.4492 (tpp) REVERT: K 242 MET cc_start: 0.5857 (tpp) cc_final: 0.5502 (tpp) REVERT: L 116 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6931 (mp10) REVERT: L 209 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: L 242 MET cc_start: 0.5850 (tpp) cc_final: 0.4754 (tpp) outliers start: 25 outliers final: 21 residues processed: 251 average time/residue: 1.5878 time to fit residues: 424.3676 Evaluate side-chains 259 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 235 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain I residue 116 GLN Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 236 GLN Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 236 GLN Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 236 GLN Chi-restraints excluded: chain L residue 116 GLN Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 209 GLU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 236 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 2.9990 chunk 111 optimal weight: 0.0000 chunk 17 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 0.0970 chunk 50 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 477 GLN B 56 GLN B 477 GLN C 56 GLN C 477 GLN D 56 GLN D 82 GLN D 477 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.178751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124800 restraints weight = 13023.994| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.89 r_work: 0.3391 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12620 Z= 0.160 Angle : 0.483 9.068 17044 Z= 0.255 Chirality : 0.039 0.132 1768 Planarity : 0.003 0.025 2264 Dihedral : 4.095 35.061 1680 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.95 % Allowed : 21.80 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.22), residues: 1504 helix: 1.78 (0.17), residues: 968 sheet: -0.07 (0.91), residues: 40 loop : 0.07 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 19 HIS 0.003 0.001 HIS D 94 PHE 0.014 0.002 PHE A 84 TYR 0.008 0.001 TYR B 115 ARG 0.003 0.000 ARG D 434 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6758.51 seconds wall clock time: 120 minutes 3.22 seconds (7203.22 seconds total)