Starting phenix.real_space_refine on Fri Dec 8 13:43:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/12_2023/8fn0_29302_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/12_2023/8fn0_29302.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/12_2023/8fn0_29302_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/12_2023/8fn0_29302_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/12_2023/8fn0_29302_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/12_2023/8fn0_29302.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/12_2023/8fn0_29302.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/12_2023/8fn0_29302_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/12_2023/8fn0_29302_updated.pdb" } resolution = 2.89 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= 0.002 sd= 0.025 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: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 5431 2.51 5 N 1424 2.21 5 O 1589 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 234": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8502 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2074 Classifications: {'peptide': 282} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 272} Chain breaks: 2 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "C" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2568 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 378 Classifications: {'peptide': 51} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1635 Classifications: {'peptide': 212} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 207} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1756 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'SRW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.89, per 1000 atoms: 0.58 Number of scatterers: 8502 At special positions: 0 Unit cell: (91.52, 117.92, 132.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 F 1 9.00 O 1589 8.00 N 1424 7.00 C 5431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.6 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 14 sheets defined 33.9% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 61 through 89 Processing helix chain 'A' and resid 101 through 128 removed outlier: 3.890A pdb=" N LEU A 106 " --> pdb=" O HIS A 103 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 119 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA A 120 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N MET A 121 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Proline residue: A 122 - end of helix removed outlier: 4.197A pdb=" N PHE A 128 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 172 Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.768A pdb=" N THR A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 207 Proline residue: A 203 - end of helix removed outlier: 4.504A pdb=" N PHE A 206 " --> pdb=" O ILE A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 Processing helix chain 'A' and resid 247 through 265 Processing helix chain 'A' and resid 302 through 333 Proline residue: A 323 - end of helix Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 341 through 372 removed outlier: 3.859A pdb=" N SER A 362 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Proline residue: A 366 - end of helix Processing helix chain 'C' and resid 4 through 24 Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'B' and resid 4 through 29 removed outlier: 3.769A pdb=" N LYS B 29 " --> pdb=" O ILE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 91 through 97 removed outlier: 4.366A pdb=" N HIS B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N CYS B 96 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE B 97 " --> pdb=" O TRP B 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 91 through 97' Processing helix chain 'B' and resid 117 through 126 Processing helix chain 'B' and resid 143 through 151 removed outlier: 4.761A pdb=" N GLU B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 182 removed outlier: 4.087A pdb=" N LYS B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 219 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 208 through 212 Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.814A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.993A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.686A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.689A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.663A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.387A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.812A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 190 through 194 removed outlier: 6.674A pdb=" N ILE B 136 " --> pdb=" O TYR B 191 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N HIS B 193 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU B 138 " --> pdb=" O HIS B 193 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE B 103 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N PHE B 139 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE B 105 " --> pdb=" O PHE B 139 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASN B 141 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 107 " --> pdb=" O ASN B 141 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 102 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N HIS B 77 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU B 33 " --> pdb=" O HIS B 77 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ARG B 79 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU B 35 " --> pdb=" O ARG B 79 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE B 81 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N GLY B 37 " --> pdb=" O PHE B 81 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.763A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 128 through 130 Processing sheet with id= M, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.452A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 213 through 219 removed outlier: 6.082A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2374 1.33 - 1.45: 1630 1.45 - 1.57: 4594 1.57 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 8680 Sorted by residual: bond pdb=" C18 SRW A 501 " pdb=" N4 SRW A 501 " ideal model delta sigma weight residual 1.484 1.362 0.122 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C13 SRW A 501 " pdb=" N1 SRW A 501 " ideal model delta sigma weight residual 1.494 1.378 0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C3 SRW A 501 " pdb=" C8 SRW A 501 " ideal model delta sigma weight residual 1.590 1.512 0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C14 SRW A 501 " pdb=" C24 SRW A 501 " ideal model delta sigma weight residual 1.553 1.484 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" N LEU A 371 " pdb=" CA LEU A 371 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.17e-02 7.31e+03 1.11e+01 ... (remaining 8675 not shown) Histogram of bond angle deviations from ideal: 59.49 - 74.43: 3 74.43 - 89.38: 0 89.38 - 104.32: 106 104.32 - 119.27: 7288 119.27 - 134.21: 4403 Bond angle restraints: 11800 Sorted by residual: angle pdb=" C24 SRW A 501 " pdb=" C14 SRW A 501 " pdb=" N3 SRW A 501 " ideal model delta sigma weight residual 71.53 118.58 -47.05 3.00e+00 1.11e-01 2.46e+02 angle pdb=" C24 SRW A 501 " pdb=" C14 SRW A 501 " pdb=" N2 SRW A 501 " ideal model delta sigma weight residual 162.48 118.21 44.27 3.00e+00 1.11e-01 2.18e+02 angle pdb=" C19 SRW A 501 " pdb=" C18 SRW A 501 " pdb=" N4 SRW A 501 " ideal model delta sigma weight residual 84.97 121.08 -36.11 3.00e+00 1.11e-01 1.45e+02 angle pdb=" C17 SRW A 501 " pdb=" C18 SRW A 501 " pdb=" N4 SRW A 501 " ideal model delta sigma weight residual 154.40 120.25 34.15 3.00e+00 1.11e-01 1.30e+02 angle pdb=" N1 SRW A 501 " pdb=" C13 SRW A 501 " pdb=" N2 SRW A 501 " ideal model delta sigma weight residual 87.58 117.04 -29.46 3.00e+00 1.11e-01 9.64e+01 ... (remaining 11795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.36: 5012 25.36 - 50.71: 56 50.71 - 76.07: 22 76.07 - 101.43: 5 101.43 - 126.78: 1 Dihedral angle restraints: 5096 sinusoidal: 1860 harmonic: 3236 Sorted by residual: dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 225 " pdb=" CB CYS A 225 " ideal model delta sinusoidal sigma weight residual 93.00 159.95 -66.95 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" C10 SRW A 501 " pdb=" C11 SRW A 501 " pdb=" N1 SRW A 501 " pdb=" C12 SRW A 501 " ideal model delta sinusoidal sigma weight residual -52.97 73.81 -126.78 1 3.00e+01 1.11e-03 1.71e+01 dihedral pdb=" CA ARG F 9 " pdb=" C ARG F 9 " pdb=" N PRO F 10 " pdb=" CA PRO F 10 " ideal model delta harmonic sigma weight residual 180.00 -162.10 -17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 5093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.365: 1368 0.365 - 0.730: 1 0.730 - 1.096: 0 1.096 - 1.461: 0 1.461 - 1.826: 2 Chirality restraints: 1371 Sorted by residual: chirality pdb=" CB ILE A 367 " pdb=" CA ILE A 367 " pdb=" CG1 ILE A 367 " pdb=" CG2 ILE A 367 " both_signs ideal model delta sigma weight residual False 2.64 0.82 1.83 2.00e-01 2.50e+01 8.34e+01 chirality pdb=" CB ILE A 364 " pdb=" CA ILE A 364 " pdb=" CG1 ILE A 364 " pdb=" CG2 ILE A 364 " both_signs ideal model delta sigma weight residual False 2.64 0.82 1.82 2.00e-01 2.50e+01 8.30e+01 chirality pdb=" C24 SRW A 501 " pdb=" C14 SRW A 501 " pdb=" C25 SRW A 501 " pdb=" F1 SRW A 501 " both_signs ideal model delta sigma weight residual True 1.88 1.42 0.45 2.00e-01 2.50e+01 5.10e+00 ... (remaining 1368 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 122 " -0.026 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C PRO A 122 " 0.089 2.00e-02 2.50e+03 pdb=" O PRO A 122 " -0.033 2.00e-02 2.50e+03 pdb=" N VAL A 123 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 124 " 0.022 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C GLU A 124 " -0.074 2.00e-02 2.50e+03 pdb=" O GLU A 124 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU A 125 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 136 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.66e+01 pdb=" C PRO E 136 " 0.070 2.00e-02 2.50e+03 pdb=" O PRO E 136 " -0.027 2.00e-02 2.50e+03 pdb=" N VAL E 137 " -0.024 2.00e-02 2.50e+03 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1464 2.76 - 3.29: 8182 3.29 - 3.83: 14143 3.83 - 4.36: 17022 4.36 - 4.90: 29661 Nonbonded interactions: 70472 Sorted by model distance: nonbonded pdb=" O MET C 325 " pdb=" ND2 ASN C 340 " model vdw 2.225 2.520 nonbonded pdb=" OH TYR A 154 " pdb=" OD1 ASN A 241 " model vdw 2.322 2.440 nonbonded pdb=" OE1 GLU C 130 " pdb=" NH2 ARG C 134 " model vdw 2.322 2.520 nonbonded pdb=" ND1 HIS D 44 " pdb=" OE2 GLU D 47 " model vdw 2.328 2.520 nonbonded pdb=" NE ARG E 148 " pdb=" O THR E 198 " model vdw 2.339 2.520 ... (remaining 70467 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.680 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: 3.730 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.560 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:11.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 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 : 0.006 0.122 8680 Z= 0.385 Angle : 1.290 47.050 11800 Z= 0.678 Chirality : 0.088 1.826 1371 Planarity : 0.006 0.084 1486 Dihedral : 10.624 126.782 3004 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.11 % Allowed : 1.36 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 1.16 (0.24), residues: 1098 helix: 0.92 (0.25), residues: 373 sheet: 1.03 (0.28), residues: 307 loop : 0.65 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP E 111 HIS 0.008 0.002 HIS C 91 PHE 0.023 0.003 PHE A 317 TYR 0.025 0.003 TYR E 102 ARG 0.015 0.001 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 223 average time/residue: 0.7235 time to fit residues: 178.5692 Evaluate side-chains 184 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 0.877 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.1842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 HIS C 91 HIS B 70 HIS B 95 HIS B 128 ASN B 141 ASN B 201 ASN B 202 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8680 Z= 0.306 Angle : 0.636 8.481 11800 Z= 0.341 Chirality : 0.045 0.175 1371 Planarity : 0.004 0.036 1486 Dihedral : 7.623 106.244 1205 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.61 % Allowed : 8.63 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 1.55 (0.25), residues: 1098 helix: 1.87 (0.26), residues: 366 sheet: 1.04 (0.28), residues: 293 loop : 0.41 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 321 HIS 0.009 0.002 HIS A 325 PHE 0.021 0.003 PHE C 253 TYR 0.026 0.002 TYR A 349 ARG 0.005 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 197 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 203 average time/residue: 0.8134 time to fit residues: 181.8563 Evaluate side-chains 195 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 184 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 6 average time/residue: 0.1247 time to fit residues: 2.4514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 0.0770 chunk 100 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN C 340 ASN B 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8680 Z= 0.265 Angle : 0.580 8.566 11800 Z= 0.312 Chirality : 0.043 0.166 1371 Planarity : 0.004 0.043 1486 Dihedral : 7.420 103.175 1205 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.84 % Allowed : 12.03 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 1.54 (0.25), residues: 1098 helix: 2.08 (0.27), residues: 363 sheet: 0.98 (0.29), residues: 293 loop : 0.24 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 169 HIS 0.006 0.001 HIS A 325 PHE 0.019 0.002 PHE C 253 TYR 0.016 0.002 TYR A 349 ARG 0.008 0.001 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 0.854 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 201 average time/residue: 0.7306 time to fit residues: 162.2128 Evaluate side-chains 199 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 0.988 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 6 residues processed: 8 average time/residue: 0.2914 time to fit residues: 4.3127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8680 Z= 0.227 Angle : 0.540 8.424 11800 Z= 0.290 Chirality : 0.043 0.176 1371 Planarity : 0.004 0.037 1486 Dihedral : 7.310 101.518 1205 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.06 % Allowed : 12.83 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 1.41 (0.25), residues: 1098 helix: 2.12 (0.27), residues: 363 sheet: 0.90 (0.30), residues: 288 loop : 0.03 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 169 HIS 0.006 0.001 HIS A 325 PHE 0.021 0.002 PHE B 146 TYR 0.015 0.001 TYR A 347 ARG 0.007 0.001 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 188 time to evaluate : 1.077 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 198 average time/residue: 0.7999 time to fit residues: 174.0801 Evaluate side-chains 199 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 186 time to evaluate : 0.893 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 6 average time/residue: 0.1565 time to fit residues: 2.6194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.0060 chunk 95 optimal weight: 0.0170 chunk 26 optimal weight: 0.7980 overall best weight: 0.4234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN B 141 ASN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8680 Z= 0.158 Angle : 0.512 8.938 11800 Z= 0.270 Chirality : 0.041 0.163 1371 Planarity : 0.003 0.035 1486 Dihedral : 7.019 98.919 1205 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.61 % Allowed : 14.30 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 (0.25), residues: 1098 helix: 2.25 (0.28), residues: 363 sheet: 1.15 (0.30), residues: 276 loop : -0.17 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 135 HIS 0.004 0.001 HIS A 325 PHE 0.022 0.001 PHE A 147 TYR 0.014 0.001 TYR A 347 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 193 time to evaluate : 0.970 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 202 average time/residue: 0.8278 time to fit residues: 183.1467 Evaluate side-chains 204 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 189 time to evaluate : 0.919 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 7 residues processed: 8 average time/residue: 0.5040 time to fit residues: 5.8983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 88 optimal weight: 0.0470 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8680 Z= 0.176 Angle : 0.526 8.401 11800 Z= 0.274 Chirality : 0.041 0.174 1371 Planarity : 0.003 0.034 1486 Dihedral : 6.906 96.868 1205 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.18 % Allowed : 15.10 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 1.42 (0.25), residues: 1098 helix: 2.27 (0.27), residues: 362 sheet: 1.11 (0.30), residues: 279 loop : -0.21 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 135 HIS 0.004 0.001 HIS A 325 PHE 0.021 0.002 PHE A 147 TYR 0.012 0.001 TYR A 347 ARG 0.008 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 195 time to evaluate : 0.854 Fit side-chains outliers start: 28 outliers final: 16 residues processed: 207 average time/residue: 0.7455 time to fit residues: 170.5824 Evaluate side-chains 207 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 191 time to evaluate : 0.838 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 7 residues processed: 9 average time/residue: 0.2328 time to fit residues: 3.8656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 0.0170 chunk 48 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8680 Z= 0.185 Angle : 0.530 8.310 11800 Z= 0.279 Chirality : 0.042 0.213 1371 Planarity : 0.003 0.035 1486 Dihedral : 6.894 96.180 1205 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.84 % Allowed : 16.23 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 1.39 (0.26), residues: 1098 helix: 2.23 (0.27), residues: 361 sheet: 0.99 (0.30), residues: 289 loop : -0.18 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A 135 HIS 0.004 0.001 HIS A 325 PHE 0.020 0.002 PHE B 146 TYR 0.011 0.001 TYR E 178 ARG 0.004 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 195 time to evaluate : 0.953 Fit side-chains outliers start: 25 outliers final: 13 residues processed: 210 average time/residue: 0.7731 time to fit residues: 179.1407 Evaluate side-chains 208 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 195 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 6 average time/residue: 0.2719 time to fit residues: 3.4352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.0050 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8680 Z= 0.187 Angle : 0.545 8.148 11800 Z= 0.286 Chirality : 0.041 0.213 1371 Planarity : 0.003 0.036 1486 Dihedral : 6.974 96.822 1205 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.27 % Allowed : 17.59 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 1.36 (0.26), residues: 1098 helix: 2.19 (0.27), residues: 361 sheet: 0.99 (0.30), residues: 289 loop : -0.19 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 135 HIS 0.004 0.001 HIS A 325 PHE 0.023 0.002 PHE B 146 TYR 0.011 0.001 TYR E 178 ARG 0.004 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 199 time to evaluate : 0.881 Fit side-chains outliers start: 20 outliers final: 15 residues processed: 210 average time/residue: 0.7674 time to fit residues: 178.5945 Evaluate side-chains 210 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 195 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 6 average time/residue: 0.2900 time to fit residues: 3.5386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 0.0670 chunk 30 optimal weight: 0.1980 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.0970 chunk 64 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN B 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8680 Z= 0.151 Angle : 0.538 7.904 11800 Z= 0.279 Chirality : 0.041 0.202 1371 Planarity : 0.003 0.041 1486 Dihedral : 6.875 95.180 1205 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.93 % Allowed : 17.93 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 1.37 (0.26), residues: 1098 helix: 2.18 (0.27), residues: 362 sheet: 1.04 (0.30), residues: 289 loop : -0.21 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 135 HIS 0.003 0.001 HIS B 77 PHE 0.023 0.001 PHE B 146 TYR 0.011 0.001 TYR A 347 ARG 0.006 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 191 time to evaluate : 0.981 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 200 average time/residue: 0.7287 time to fit residues: 161.4132 Evaluate side-chains 202 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 190 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.0947 time to fit residues: 1.7835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.1980 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN B 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8680 Z= 0.212 Angle : 0.574 8.618 11800 Z= 0.299 Chirality : 0.042 0.185 1371 Planarity : 0.004 0.039 1486 Dihedral : 6.858 94.826 1205 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.59 % Allowed : 18.96 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 1.25 (0.25), residues: 1098 helix: 2.09 (0.27), residues: 362 sheet: 0.92 (0.30), residues: 290 loop : -0.23 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 135 HIS 0.005 0.001 HIS B 77 PHE 0.024 0.002 PHE B 146 TYR 0.012 0.001 TYR E 178 ARG 0.005 0.000 ARG A 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 196 time to evaluate : 0.807 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 205 average time/residue: 0.7006 time to fit residues: 159.1452 Evaluate side-chains 203 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 193 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.1003 time to fit residues: 1.5946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 365 ASN B 141 ASN E 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.140693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.118227 restraints weight = 12231.656| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.19 r_work: 0.3393 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8680 Z= 0.234 Angle : 0.586 8.499 11800 Z= 0.305 Chirality : 0.043 0.200 1371 Planarity : 0.004 0.039 1486 Dihedral : 6.842 94.583 1205 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.59 % Allowed : 18.73 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 1.17 (0.25), residues: 1098 helix: 2.04 (0.27), residues: 362 sheet: 0.90 (0.30), residues: 290 loop : -0.32 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 135 HIS 0.005 0.001 HIS A 325 PHE 0.024 0.002 PHE B 146 TYR 0.012 0.001 TYR E 178 ARG 0.005 0.000 ARG A 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3563.62 seconds wall clock time: 63 minutes 55.23 seconds (3835.23 seconds total)