Starting phenix.real_space_refine on Mon Mar 11 14:48:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/03_2024/8fn0_29302_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/03_2024/8fn0_29302.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/03_2024/8fn0_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_29302/03_2024/8fn0_29302_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/03_2024/8fn0_29302_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/03_2024/8fn0_29302.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/03_2024/8fn0_29302.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/03_2024/8fn0_29302_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn0_29302/03_2024/8fn0_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.90, 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: 3.17 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: 1.65 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: 2.59 Time building geometry restraints manager: 3.45 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: 1.170 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: 3.880 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.930 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.520 ------------------------------------------------------------------------------- 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 : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.7888 (mt) cc_final: 0.7685 (tm) REVERT: A 238 ILE cc_start: 0.7891 (tp) cc_final: 0.7662 (tp) REVERT: A 250 MET cc_start: 0.7103 (tpp) cc_final: 0.6826 (tpt) REVERT: A 343 LEU cc_start: 0.8181 (tp) cc_final: 0.7866 (tt) REVERT: A 350 PHE cc_start: 0.7245 (t80) cc_final: 0.6821 (t80) REVERT: C 37 ILE cc_start: 0.8089 (mt) cc_final: 0.7822 (pt) REVERT: C 38 ASP cc_start: 0.7789 (m-30) cc_final: 0.7575 (m-30) REVERT: C 227 SER cc_start: 0.8406 (t) cc_final: 0.8106 (m) REVERT: C 262 MET cc_start: 0.8018 (tpp) cc_final: 0.7713 (tpp) REVERT: C 314 ARG cc_start: 0.8538 (ttm170) cc_final: 0.8186 (ttm170) REVERT: B 32 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8572 (mtmp) REVERT: B 66 ILE cc_start: 0.8160 (mt) cc_final: 0.7937 (mm) REVERT: E 17 SER cc_start: 0.8268 (p) cc_final: 0.7995 (m) REVERT: E 23 SER cc_start: 0.8303 (t) cc_final: 0.8043 (m) REVERT: E 25 SER cc_start: 0.8304 (t) cc_final: 0.8079 (p) REVERT: E 192 SER cc_start: 0.8549 (t) cc_final: 0.8330 (p) REVERT: E 211 ASP cc_start: 0.7989 (t0) cc_final: 0.7692 (t0) REVERT: E 218 MET cc_start: 0.8279 (ttp) cc_final: 0.7914 (ttp) outliers start: 1 outliers final: 1 residues processed: 223 average time/residue: 0.7146 time to fit residues: 176.1042 Evaluate side-chains 187 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU 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: 0.9980 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.7700 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8680 Z= 0.273 Angle : 0.605 8.068 11800 Z= 0.325 Chirality : 0.044 0.172 1371 Planarity : 0.004 0.040 1486 Dihedral : 7.573 105.644 1207 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.27 % Allowed : 7.72 % Favored : 90.01 % 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: 1.62 (0.25), residues: 1098 helix: 1.93 (0.26), residues: 367 sheet: 1.03 (0.28), residues: 293 loop : 0.48 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 169 HIS 0.007 0.001 HIS A 325 PHE 0.020 0.002 PHE C 253 TYR 0.023 0.002 TYR A 349 ARG 0.005 0.000 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 218 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 198 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.7810 (mt) cc_final: 0.7513 (tm) REVERT: A 244 MET cc_start: 0.7762 (mmm) cc_final: 0.7496 (mmm) REVERT: A 250 MET cc_start: 0.7037 (tpp) cc_final: 0.6789 (tpt) REVERT: A 340 THR cc_start: 0.8026 (p) cc_final: 0.7667 (t) REVERT: A 347 TYR cc_start: 0.7092 (t80) cc_final: 0.6886 (t80) REVERT: A 350 PHE cc_start: 0.7107 (t80) cc_final: 0.6684 (t80) REVERT: C 22 ARG cc_start: 0.7437 (mtt180) cc_final: 0.7229 (mtt180) REVERT: C 37 ILE cc_start: 0.8073 (mt) cc_final: 0.7783 (pt) REVERT: C 38 ASP cc_start: 0.7744 (m-30) cc_final: 0.7523 (m-30) REVERT: C 49 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7331 (mpt-90) REVERT: C 158 VAL cc_start: 0.8457 (p) cc_final: 0.8138 (t) REVERT: C 214 ARG cc_start: 0.6909 (mpt180) cc_final: 0.6292 (mpt180) REVERT: C 217 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7102 (ppp) REVERT: B 66 ILE cc_start: 0.8210 (mt) cc_final: 0.7969 (mm) REVERT: B 108 ASP cc_start: 0.7478 (t0) cc_final: 0.7254 (t0) REVERT: E 17 SER cc_start: 0.8130 (p) cc_final: 0.7893 (m) REVERT: E 23 SER cc_start: 0.8269 (t) cc_final: 0.8001 (m) REVERT: E 63 THR cc_start: 0.8301 (p) cc_final: 0.8079 (t) REVERT: E 192 SER cc_start: 0.8562 (t) cc_final: 0.8306 (p) REVERT: E 211 ASP cc_start: 0.7950 (t0) cc_final: 0.7663 (t0) outliers start: 20 outliers final: 9 residues processed: 203 average time/residue: 0.7628 time to fit residues: 170.3412 Evaluate side-chains 198 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 187 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 ASN B 141 ASN B 201 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2109 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= 0.253 Angle : 0.558 8.659 11800 Z= 0.300 Chirality : 0.043 0.167 1371 Planarity : 0.004 0.043 1486 Dihedral : 7.414 105.292 1205 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.27 % Allowed : 10.67 % Favored : 87.06 % 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: 1.53 (0.25), residues: 1098 helix: 2.10 (0.27), residues: 362 sheet: 0.94 (0.29), residues: 288 loop : 0.25 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 169 HIS 0.007 0.001 HIS A 325 PHE 0.020 0.002 PHE C 253 TYR 0.018 0.002 TYR A 349 ARG 0.010 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 226 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 206 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 250 MET cc_start: 0.7012 (tpp) cc_final: 0.6769 (tpt) REVERT: A 371 LEU cc_start: 0.7898 (tp) cc_final: 0.7644 (tt) REVERT: C 22 ARG cc_start: 0.7376 (mtt180) cc_final: 0.7174 (mtt180) REVERT: C 158 VAL cc_start: 0.8402 (p) cc_final: 0.8151 (t) REVERT: C 217 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7877 (pmm) REVERT: B 66 ILE cc_start: 0.8229 (mt) cc_final: 0.7995 (mm) REVERT: B 108 ASP cc_start: 0.7546 (t0) cc_final: 0.7261 (t0) REVERT: E 17 SER cc_start: 0.8114 (p) cc_final: 0.7897 (m) REVERT: E 23 SER cc_start: 0.8264 (t) cc_final: 0.7980 (m) REVERT: E 63 THR cc_start: 0.8367 (p) cc_final: 0.8155 (t) REVERT: E 192 SER cc_start: 0.8523 (t) cc_final: 0.8280 (p) REVERT: E 211 ASP cc_start: 0.7937 (t0) cc_final: 0.7637 (t0) outliers start: 20 outliers final: 14 residues processed: 210 average time/residue: 0.7368 time to fit residues: 170.6277 Evaluate side-chains 216 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 201 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN B 141 ASN B 201 ASN E 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8680 Z= 0.211 Angle : 0.520 8.552 11800 Z= 0.280 Chirality : 0.042 0.170 1371 Planarity : 0.004 0.036 1486 Dihedral : 7.281 104.460 1205 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.84 % Allowed : 12.49 % Favored : 84.68 % 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: 1.51 (0.25), residues: 1098 helix: 2.20 (0.27), residues: 362 sheet: 0.94 (0.29), residues: 286 loop : 0.12 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 135 HIS 0.005 0.001 HIS A 325 PHE 0.021 0.002 PHE B 146 TYR 0.013 0.001 TYR A 349 ARG 0.005 0.001 ARG F 9 *********************** 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 228 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 203 time to evaluate : 1.151 Fit side-chains REVERT: A 250 MET cc_start: 0.6950 (tpp) cc_final: 0.6742 (tpt) REVERT: A 259 VAL cc_start: 0.8318 (t) cc_final: 0.8044 (t) REVERT: A 371 LEU cc_start: 0.7923 (tp) cc_final: 0.7691 (tt) REVERT: C 158 VAL cc_start: 0.8385 (p) cc_final: 0.8161 (t) REVERT: C 217 MET cc_start: 0.8138 (ppp) cc_final: 0.7901 (pmm) REVERT: B 66 ILE cc_start: 0.8243 (mt) cc_final: 0.7984 (mm) REVERT: B 108 ASP cc_start: 0.7574 (t0) cc_final: 0.7231 (t0) REVERT: B 115 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.6996 (mmm) REVERT: E 23 SER cc_start: 0.8271 (t) cc_final: 0.7970 (m) REVERT: E 63 THR cc_start: 0.8388 (p) cc_final: 0.8182 (t) REVERT: E 192 SER cc_start: 0.8514 (t) cc_final: 0.8271 (p) REVERT: E 211 ASP cc_start: 0.7911 (t0) cc_final: 0.7592 (t0) outliers start: 25 outliers final: 16 residues processed: 210 average time/residue: 0.7516 time to fit residues: 173.6749 Evaluate side-chains 220 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 203 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.0060 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.0060 chunk 95 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 overall best weight: 0.3812 ------------------------------------------------------------------------------- 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: 0.7665 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8680 Z= 0.145 Angle : 0.481 8.230 11800 Z= 0.257 Chirality : 0.040 0.162 1371 Planarity : 0.003 0.035 1486 Dihedral : 7.038 103.374 1205 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.38 % Allowed : 13.62 % Favored : 84.00 % 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: 1.59 (0.25), residues: 1098 helix: 2.37 (0.27), residues: 362 sheet: 1.21 (0.30), residues: 273 loop : -0.07 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 135 HIS 0.003 0.001 HIS B 77 PHE 0.023 0.001 PHE A 147 TYR 0.011 0.001 TYR E 178 ARG 0.004 0.000 ARG F 9 *********************** 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 224 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 203 time to evaluate : 1.033 Fit side-chains REVERT: A 241 ASN cc_start: 0.7568 (t0) cc_final: 0.7286 (t0) REVERT: A 259 VAL cc_start: 0.8283 (t) cc_final: 0.8009 (t) REVERT: C 158 VAL cc_start: 0.8341 (p) cc_final: 0.8130 (t) REVERT: C 290 ASP cc_start: 0.7295 (OUTLIER) cc_final: 0.6991 (p0) REVERT: B 108 ASP cc_start: 0.7554 (t0) cc_final: 0.7202 (t0) REVERT: E 23 SER cc_start: 0.8237 (t) cc_final: 0.7947 (m) REVERT: E 63 THR cc_start: 0.8397 (p) cc_final: 0.8195 (t) REVERT: E 110 PHE cc_start: 0.8473 (t80) cc_final: 0.8030 (t80) REVERT: E 192 SER cc_start: 0.8493 (t) cc_final: 0.8261 (p) REVERT: E 211 ASP cc_start: 0.7863 (t0) cc_final: 0.7554 (t0) outliers start: 21 outliers final: 11 residues processed: 210 average time/residue: 0.7040 time to fit residues: 163.8395 Evaluate side-chains 213 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 201 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain E residue 25 SER 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: 0.0670 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 0.0980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN B 141 ASN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8680 Z= 0.174 Angle : 0.504 8.838 11800 Z= 0.266 Chirality : 0.041 0.179 1371 Planarity : 0.003 0.035 1486 Dihedral : 6.983 102.279 1205 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.95 % Allowed : 15.21 % Favored : 81.84 % 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: 2.37 (0.27), residues: 361 sheet: 1.12 (0.30), residues: 279 loop : -0.10 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 135 HIS 0.004 0.001 HIS A 325 PHE 0.020 0.002 PHE B 146 TYR 0.012 0.001 TYR E 178 ARG 0.009 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 225 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 199 time to evaluate : 0.912 Fit side-chains REVERT: A 204 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6476 (tmt) REVERT: A 241 ASN cc_start: 0.7578 (t0) cc_final: 0.7292 (t0) REVERT: A 259 VAL cc_start: 0.8298 (t) cc_final: 0.8054 (t) REVERT: C 98 SER cc_start: 0.8363 (p) cc_final: 0.7882 (t) REVERT: C 158 VAL cc_start: 0.8348 (p) cc_final: 0.8105 (t) REVERT: C 290 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.7004 (p0) REVERT: B 108 ASP cc_start: 0.7553 (t0) cc_final: 0.7179 (t0) REVERT: B 115 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6878 (mmm) REVERT: E 23 SER cc_start: 0.8262 (t) cc_final: 0.7964 (m) REVERT: E 63 THR cc_start: 0.8406 (p) cc_final: 0.8201 (t) REVERT: E 110 PHE cc_start: 0.8504 (t80) cc_final: 0.8058 (t80) REVERT: E 187 VAL cc_start: 0.8087 (t) cc_final: 0.7866 (m) REVERT: E 192 SER cc_start: 0.8491 (t) cc_final: 0.8290 (p) REVERT: E 211 ASP cc_start: 0.7861 (t0) cc_final: 0.7510 (t0) outliers start: 26 outliers final: 12 residues processed: 210 average time/residue: 0.7139 time to fit residues: 166.0194 Evaluate side-chains 214 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 199 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 0.0470 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- 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: 0.7699 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8680 Z= 0.229 Angle : 0.524 8.908 11800 Z= 0.281 Chirality : 0.042 0.202 1371 Planarity : 0.004 0.045 1486 Dihedral : 7.101 102.515 1205 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.38 % Allowed : 16.00 % Favored : 81.61 % 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: 1.38 (0.25), residues: 1098 helix: 2.23 (0.27), residues: 363 sheet: 0.88 (0.29), residues: 294 loop : -0.13 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 135 HIS 0.005 0.001 HIS A 325 PHE 0.020 0.002 PHE B 146 TYR 0.012 0.001 TYR E 178 ARG 0.009 0.001 ARG F 9 *********************** 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 227 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 206 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 204 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.6626 (tmt) REVERT: A 241 ASN cc_start: 0.7593 (t0) cc_final: 0.7288 (t0) REVERT: A 259 VAL cc_start: 0.8330 (t) cc_final: 0.8078 (t) REVERT: C 98 SER cc_start: 0.8369 (p) cc_final: 0.7887 (t) REVERT: C 158 VAL cc_start: 0.8378 (p) cc_final: 0.8132 (t) REVERT: C 290 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.7051 (p0) REVERT: B 108 ASP cc_start: 0.7544 (t0) cc_final: 0.7172 (t0) REVERT: B 115 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6911 (mmm) REVERT: E 23 SER cc_start: 0.8270 (t) cc_final: 0.7969 (m) REVERT: E 63 THR cc_start: 0.8390 (p) cc_final: 0.8171 (t) REVERT: E 110 PHE cc_start: 0.8555 (t80) cc_final: 0.8149 (t80) REVERT: E 192 SER cc_start: 0.8505 (t) cc_final: 0.8290 (p) REVERT: E 211 ASP cc_start: 0.7910 (t0) cc_final: 0.7523 (t0) outliers start: 21 outliers final: 10 residues processed: 214 average time/residue: 0.7255 time to fit residues: 171.9828 Evaluate side-chains 219 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 206 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.0020 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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: 0.7684 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8680 Z= 0.184 Angle : 0.515 8.674 11800 Z= 0.271 Chirality : 0.041 0.163 1371 Planarity : 0.003 0.035 1486 Dihedral : 7.040 102.186 1205 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.38 % Allowed : 17.14 % Favored : 80.48 % 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 (0.25), residues: 1098 helix: 2.26 (0.27), residues: 363 sheet: 0.93 (0.30), residues: 290 loop : -0.18 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 135 HIS 0.005 0.001 HIS A 325 PHE 0.022 0.001 PHE B 146 TYR 0.011 0.001 TYR E 178 ARG 0.008 0.000 ARG F 9 *********************** 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 229 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 208 time to evaluate : 1.003 Fit side-chains REVERT: A 158 LEU cc_start: 0.8645 (mm) cc_final: 0.8430 (mm) REVERT: A 204 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.6539 (tmt) REVERT: A 241 ASN cc_start: 0.7608 (t0) cc_final: 0.7302 (t0) REVERT: A 259 VAL cc_start: 0.8336 (t) cc_final: 0.8088 (t) REVERT: C 98 SER cc_start: 0.8375 (p) cc_final: 0.7905 (t) REVERT: C 158 VAL cc_start: 0.8368 (p) cc_final: 0.8072 (t) REVERT: C 290 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.7016 (p0) REVERT: B 108 ASP cc_start: 0.7537 (t0) cc_final: 0.7154 (t0) REVERT: B 115 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6849 (mmm) REVERT: B 224 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7399 (tp) REVERT: E 23 SER cc_start: 0.8238 (t) cc_final: 0.7956 (m) REVERT: E 63 THR cc_start: 0.8356 (p) cc_final: 0.8120 (t) REVERT: E 110 PHE cc_start: 0.8510 (t80) cc_final: 0.8097 (t80) REVERT: E 192 SER cc_start: 0.8505 (t) cc_final: 0.8286 (p) REVERT: E 211 ASP cc_start: 0.7897 (t0) cc_final: 0.7524 (t0) outliers start: 21 outliers final: 12 residues processed: 216 average time/residue: 0.7161 time to fit residues: 170.9654 Evaluate side-chains 218 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 202 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 0.1980 chunk 63 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7698 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8680 Z= 0.219 Angle : 0.534 8.830 11800 Z= 0.283 Chirality : 0.042 0.164 1371 Planarity : 0.003 0.036 1486 Dihedral : 7.080 101.324 1205 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.04 % Allowed : 16.91 % Favored : 81.04 % 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: 1.27 (0.25), residues: 1098 helix: 2.18 (0.27), residues: 363 sheet: 0.86 (0.30), residues: 291 loop : -0.26 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 135 HIS 0.005 0.001 HIS A 325 PHE 0.023 0.002 PHE B 146 TYR 0.012 0.001 TYR E 178 ARG 0.007 0.001 ARG F 9 *********************** 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 225 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 207 time to evaluate : 1.062 Fit side-chains REVERT: A 119 LEU cc_start: 0.8433 (mp) cc_final: 0.8176 (mm) REVERT: A 158 LEU cc_start: 0.8582 (mm) cc_final: 0.8375 (mm) REVERT: A 204 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6555 (tmt) REVERT: A 241 ASN cc_start: 0.7598 (t0) cc_final: 0.7320 (t0) REVERT: A 259 VAL cc_start: 0.8313 (t) cc_final: 0.8089 (t) REVERT: C 98 SER cc_start: 0.8368 (p) cc_final: 0.7892 (t) REVERT: C 137 ARG cc_start: 0.7354 (tpp80) cc_final: 0.6783 (tpp80) REVERT: C 158 VAL cc_start: 0.8367 (p) cc_final: 0.8082 (t) REVERT: C 290 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.7029 (p0) REVERT: B 108 ASP cc_start: 0.7536 (t0) cc_final: 0.7158 (t0) REVERT: B 115 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6810 (mtp) REVERT: E 23 SER cc_start: 0.8259 (t) cc_final: 0.7964 (m) REVERT: E 63 THR cc_start: 0.8346 (p) cc_final: 0.8096 (t) REVERT: E 110 PHE cc_start: 0.8553 (t80) cc_final: 0.8150 (t80) REVERT: E 192 SER cc_start: 0.8535 (t) cc_final: 0.8313 (p) REVERT: E 211 ASP cc_start: 0.7946 (t0) cc_final: 0.7537 (t0) outliers start: 18 outliers final: 10 residues processed: 215 average time/residue: 0.6952 time to fit residues: 165.0533 Evaluate side-chains 219 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 206 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.0370 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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: 0.7685 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8680 Z= 0.187 Angle : 0.520 8.711 11800 Z= 0.276 Chirality : 0.042 0.206 1371 Planarity : 0.003 0.037 1486 Dihedral : 7.020 101.367 1205 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.36 % Allowed : 17.59 % Favored : 81.04 % 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 (0.26), residues: 1098 helix: 2.19 (0.27), residues: 362 sheet: 0.78 (0.30), residues: 293 loop : -0.23 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 135 HIS 0.004 0.001 HIS B 77 PHE 0.023 0.001 PHE B 146 TYR 0.012 0.001 TYR A 324 ARG 0.010 0.001 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 222 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 210 time to evaluate : 0.939 Fit side-chains REVERT: A 158 LEU cc_start: 0.8635 (mm) cc_final: 0.8418 (mm) REVERT: A 204 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6517 (tmt) REVERT: A 241 ASN cc_start: 0.7550 (t0) cc_final: 0.7260 (t0) REVERT: A 259 VAL cc_start: 0.8332 (t) cc_final: 0.8097 (t) REVERT: C 98 SER cc_start: 0.8371 (p) cc_final: 0.7895 (t) REVERT: C 137 ARG cc_start: 0.7347 (tpp80) cc_final: 0.6765 (tpp80) REVERT: C 158 VAL cc_start: 0.8363 (p) cc_final: 0.8077 (t) REVERT: C 290 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.7010 (p0) REVERT: B 108 ASP cc_start: 0.7529 (t0) cc_final: 0.7143 (t0) REVERT: B 115 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6824 (mmm) REVERT: E 23 SER cc_start: 0.8232 (t) cc_final: 0.7957 (m) REVERT: E 63 THR cc_start: 0.8362 (p) cc_final: 0.8105 (t) REVERT: E 110 PHE cc_start: 0.8520 (t80) cc_final: 0.8110 (t80) REVERT: E 192 SER cc_start: 0.8527 (t) cc_final: 0.8308 (p) REVERT: E 211 ASP cc_start: 0.7923 (t0) cc_final: 0.7496 (t0) outliers start: 12 outliers final: 8 residues processed: 216 average time/residue: 0.6880 time to fit residues: 164.7983 Evaluate side-chains 218 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 207 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 0.0010 chunk 89 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.141361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118974 restraints weight = 12234.319| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.20 r_work: 0.3407 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8680 Z= 0.191 Angle : 0.528 8.638 11800 Z= 0.277 Chirality : 0.041 0.164 1371 Planarity : 0.003 0.037 1486 Dihedral : 6.988 100.144 1205 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.70 % Allowed : 18.05 % Favored : 80.25 % 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: 2.24 (0.27), residues: 359 sheet: 0.75 (0.30), residues: 293 loop : -0.25 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 135 HIS 0.004 0.001 HIS B 77 PHE 0.023 0.002 PHE B 146 TYR 0.012 0.001 TYR E 178 ARG 0.007 0.000 ARG A 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3560.37 seconds wall clock time: 63 minutes 52.89 seconds (3832.89 seconds total)