Starting phenix.real_space_refine on Fri Nov 17 14:33:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znn_11318/11_2023/6znn_11318_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znn_11318/11_2023/6znn_11318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znn_11318/11_2023/6znn_11318.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znn_11318/11_2023/6znn_11318.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znn_11318/11_2023/6znn_11318_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znn_11318/11_2023/6znn_11318_neut_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 9 5.49 5 S 97 5.16 5 C 12313 2.51 5 N 3417 2.21 5 O 3618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 87": "OE1" <-> "OE2" Residue "G ARG 121": "NH1" <-> "NH2" Residue "G ARG 199": "NH1" <-> "NH2" Residue "G GLU 237": "OE1" <-> "OE2" Residue "G GLU 270": "OE1" <-> "OE2" Residue "G ARG 291": "NH1" <-> "NH2" Residue "G ARG 329": "NH1" <-> "NH2" Residue "G ARG 369": "NH1" <-> "NH2" Residue "H TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 177": "NH1" <-> "NH2" Residue "H ARG 183": "NH1" <-> "NH2" Residue "H GLU 226": "OE1" <-> "OE2" Residue "H GLU 316": "OE1" <-> "OE2" Residue "I GLU 237": "OE1" <-> "OE2" Residue "I ARG 373": "NH1" <-> "NH2" Residue "J GLU 22": "OE1" <-> "OE2" Residue "J ARG 85": "NH1" <-> "NH2" Residue "J GLU 114": "OE1" <-> "OE2" Residue "J GLU 204": "OE1" <-> "OE2" Residue "J GLU 253": "OE1" <-> "OE2" Residue "J ARG 263": "NH1" <-> "NH2" Residue "J GLU 276": "OE1" <-> "OE2" Residue "M ARG 74": "NH1" <-> "NH2" Residue "M GLU 84": "OE1" <-> "OE2" Residue "U GLU 22": "OE1" <-> "OE2" Residue "U GLU 44": "OE1" <-> "OE2" Residue "U GLU 52": "OE1" <-> "OE2" Residue "U GLU 58": "OE1" <-> "OE2" Residue "U GLU 91": "OE1" <-> "OE2" Residue "U GLU 135": "OE1" <-> "OE2" Residue "U GLU 139": "OE1" <-> "OE2" Residue "U ARG 151": "NH1" <-> "NH2" Residue "V ARG 24": "NH1" <-> "NH2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "Y ARG 31": "NH1" <-> "NH2" Residue "Y ARG 37": "NH1" <-> "NH2" Residue "Y GLU 45": "OE1" <-> "OE2" Residue "Y GLU 56": "OE1" <-> "OE2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ARG 119": "NH1" <-> "NH2" Residue "Y GLU 149": "OE1" <-> "OE2" Residue "Y GLU 161": "OE1" <-> "OE2" Residue "Y ARG 164": "NH1" <-> "NH2" Residue "Y ARG 255": "NH1" <-> "NH2" Residue "Y ARG 272": "NH1" <-> "NH2" Residue "Y ARG 280": "NH1" <-> "NH2" Residue "Y ARG 285": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 19457 Number of models: 1 Model: "" Number of chains: 17 Chain: "G" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2956 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "H" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2885 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "I" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2941 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2932 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 354} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "M" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 583 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 340 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'TRANS': 67} Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 68 Planarities with less than four sites: {'UNK:plan-1': 68} Unresolved non-hydrogen planarities: 68 Chain: "T" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 340 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'TRANS': 67} Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 68 Planarities with less than four sites: {'UNK:plan-1': 68} Unresolved non-hydrogen planarities: 68 Chain: "U" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1224 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 154} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "V" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1260 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 10, 'TRANS': 168} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 85 Chain: "X" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 465 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'TRANS': 92} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'UNK:plan-1': 93} Unresolved non-hydrogen planarities: 93 Chain: "Y" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 2956 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 30, 'TRANS': 379} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 335 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 14, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 219 Chain: "x" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 460 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'TRANS': 91} Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 276 Unresolved non-hydrogen dihedrals: 92 Planarities with less than four sites: {'UNK:plan-1': 92} Unresolved non-hydrogen planarities: 92 Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16189 SG CYS Y 33 81.546 41.291 50.527 1.00176.12 S ATOM 17746 SG CYS Y 287 82.674 38.608 52.763 1.00182.93 S ATOM 16324 SG CYS Y 51 112.896 30.834 68.620 1.00172.70 S ATOM 16468 SG CYS Y 70 112.797 27.626 71.431 1.00168.75 S ATOM 16509 SG CYS Y 76 121.782 39.737 72.509 1.00177.86 S ATOM 16664 SG CYS Y 114 125.834 42.054 72.654 1.00177.90 S Time building chain proxies: 10.95, per 1000 atoms: 0.56 Number of scatterers: 19457 At special positions: 0 Unit cell: (171.52, 119.26, 176.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 97 16.00 P 9 15.00 O 3618 8.00 N 3417 7.00 C 12313 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.68 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y 501 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 287 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 33 " pdb=" ZN Y 502 " pdb="ZN ZN Y 502 " - pdb=" SG CYS Y 51 " pdb="ZN ZN Y 502 " - pdb=" SG CYS Y 70 " pdb=" ZN Y 503 " pdb="ZN ZN Y 503 " - pdb=" SG CYS Y 114 " pdb="ZN ZN Y 503 " - pdb=" SG CYS Y 76 " 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4970 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 79 helices and 26 sheets defined 43.4% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'G' and resid 60 through 64 Processing helix chain 'G' and resid 83 through 94 removed outlier: 3.580A pdb=" N TYR G 94 " --> pdb=" O TRP G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 130 Processing helix chain 'G' and resid 142 through 150 removed outlier: 3.688A pdb=" N TYR G 148 " --> pdb=" O VAL G 144 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 201 Processing helix chain 'G' and resid 208 through 220 removed outlier: 3.844A pdb=" N GLU G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE G 213 " --> pdb=" O SER G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 233 removed outlier: 3.610A pdb=" N THR G 233 " --> pdb=" O GLN G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 262 removed outlier: 3.666A pdb=" N ARG G 255 " --> pdb=" O GLY G 252 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG G 257 " --> pdb=" O SER G 254 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA G 258 " --> pdb=" O ARG G 255 " (cutoff:3.500A) Proline residue: G 259 - end of helix Processing helix chain 'G' and resid 275 through 285 removed outlier: 3.573A pdb=" N VAL G 280 " --> pdb=" O HIS G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 296 removed outlier: 4.312A pdb=" N ARG G 292 " --> pdb=" O ASP G 289 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE G 295 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER G 296 " --> pdb=" O THR G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 305 No H-bonds generated for 'chain 'G' and resid 303 through 305' Processing helix chain 'G' and resid 310 through 321 removed outlier: 3.529A pdb=" N LYS G 319 " --> pdb=" O LEU G 315 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS G 320 " --> pdb=" O SER G 316 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 321 " --> pdb=" O GLU G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 349 Processing helix chain 'G' and resid 351 through 356 Processing helix chain 'G' and resid 360 through 366 Processing helix chain 'G' and resid 368 through 374 Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'H' and resid 79 through 90 Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 137 through 145 removed outlier: 3.702A pdb=" N LEU H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR H 143 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA H 144 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 196 removed outlier: 3.606A pdb=" N LYS H 191 " --> pdb=" O ASP H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 216 Processing helix chain 'H' and resid 223 through 232 Processing helix chain 'H' and resid 251 through 262 removed outlier: 3.537A pdb=" N ARG H 256 " --> pdb=" O GLU H 253 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS H 257 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 274 through 284 removed outlier: 3.629A pdb=" N THR H 278 " --> pdb=" O ILE H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 289 through 295 Processing helix chain 'H' and resid 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 309 through 320 Processing helix chain 'H' and resid 338 through 348 removed outlier: 3.542A pdb=" N GLY H 342 " --> pdb=" O SER H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 354 removed outlier: 3.500A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 365 Processing helix chain 'H' and resid 367 through 372 Processing helix chain 'I' and resid 60 through 64 Processing helix chain 'I' and resid 83 through 93 Processing helix chain 'I' and resid 118 through 130 Processing helix chain 'I' and resid 142 through 150 removed outlier: 3.691A pdb=" N LEU I 147 " --> pdb=" O ALA I 143 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR I 148 " --> pdb=" O VAL I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 201 Processing helix chain 'I' and resid 208 through 220 removed outlier: 3.793A pdb=" N GLU I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE I 213 " --> pdb=" O SER I 209 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL I 214 " --> pdb=" O GLU I 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 233 Processing helix chain 'I' and resid 252 through 263 removed outlier: 3.804A pdb=" N ARG I 257 " --> pdb=" O SER I 254 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA I 258 " --> pdb=" O ARG I 255 " (cutoff:3.500A) Proline residue: I 259 - end of helix Processing helix chain 'I' and resid 275 through 285 removed outlier: 3.593A pdb=" N LEU I 279 " --> pdb=" O ILE I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 296 removed outlier: 4.605A pdb=" N ARG I 292 " --> pdb=" O MET I 288 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N THR I 293 " --> pdb=" O ASP I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 321 removed outlier: 3.505A pdb=" N SER I 316 " --> pdb=" O ASP I 312 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS I 320 " --> pdb=" O SER I 316 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU I 321 " --> pdb=" O GLU I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 349 removed outlier: 3.504A pdb=" N GLY I 344 " --> pdb=" O THR I 340 " (cutoff:3.500A) Processing helix chain 'I' and resid 353 through 356 No H-bonds generated for 'chain 'I' and resid 353 through 356' Processing helix chain 'I' and resid 360 through 366 Processing helix chain 'I' and resid 369 through 375 Processing helix chain 'J' and resid 61 through 77 Processing helix chain 'J' and resid 99 through 111 Processing helix chain 'J' and resid 123 through 131 removed outlier: 3.584A pdb=" N LEU J 129 " --> pdb=" O LEU J 125 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR J 130 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU J 131 " --> pdb=" O ALA J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 160 No H-bonds generated for 'chain 'J' and resid 158 through 160' Processing helix chain 'J' and resid 168 through 181 Processing helix chain 'J' and resid 204 through 213 Processing helix chain 'J' and resid 220 through 231 removed outlier: 3.564A pdb=" N LYS J 225 " --> pdb=" O THR J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 260 through 271 removed outlier: 3.925A pdb=" N ASP J 264 " --> pdb=" O GLY J 260 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL J 267 " --> pdb=" O ARG J 263 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU J 268 " --> pdb=" O ASP J 264 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE J 269 " --> pdb=" O SER J 265 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU J 270 " --> pdb=" O VAL J 266 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE J 271 " --> pdb=" O VAL J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 290 removed outlier: 4.236A pdb=" N ILE J 284 " --> pdb=" O VAL J 280 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU J 285 " --> pdb=" O ALA J 281 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN J 290 " --> pdb=" O ASP J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 296 through 301 Processing helix chain 'J' and resid 308 through 311 Processing helix chain 'J' and resid 315 through 328 removed outlier: 3.850A pdb=" N GLU J 328 " --> pdb=" O ARG J 324 " (cutoff:3.500A) Processing helix chain 'J' and resid 330 through 333 No H-bonds generated for 'chain 'J' and resid 330 through 333' Processing helix chain 'J' and resid 350 through 352 No H-bonds generated for 'chain 'J' and resid 350 through 352' Processing helix chain 'J' and resid 354 through 362 removed outlier: 3.634A pdb=" N GLY J 358 " --> pdb=" O ALA J 354 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 371 removed outlier: 4.042A pdb=" N SER J 370 " --> pdb=" O ASP J 366 " (cutoff:3.500A) Processing helix chain 'J' and resid 375 through 381 Processing helix chain 'M' and resid 4 through 8 removed outlier: 3.584A pdb=" N ASP M 8 " --> pdb=" O PRO M 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 4 through 8' Processing helix chain 'M' and resid 52 through 59 removed outlier: 3.504A pdb=" N ASP M 57 " --> pdb=" O ASN M 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 67 Processing helix chain 'T' and resid 2 through 67 removed outlier: 4.162A pdb=" N UNK T 27 " --> pdb=" O UNK T 23 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 69 No H-bonds generated for 'chain 'U' and resid 66 through 69' Processing helix chain 'U' and resid 162 through 170 removed outlier: 3.927A pdb=" N MET U 168 " --> pdb=" O LEU U 164 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS U 169 " --> pdb=" O ASP U 165 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE U 170 " --> pdb=" O PHE U 166 " (cutoff:3.500A) Processing helix chain 'V' and resid 162 through 175 removed outlier: 4.141A pdb=" N ILE V 166 " --> pdb=" O GLN V 162 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP V 167 " --> pdb=" O GLU V 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 132 through 220 removed outlier: 3.929A pdb=" N UNK X 148 " --> pdb=" O UNK X 144 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N UNK X 154 " --> pdb=" O UNK X 150 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N UNK X 161 " --> pdb=" O UNK X 157 " (cutoff:3.500A) Processing helix chain 'Y' and resid 60 through 66 Processing helix chain 'Y' and resid 118 through 121 No H-bonds generated for 'chain 'Y' and resid 118 through 121' Processing helix chain 'Y' and resid 142 through 171 removed outlier: 3.517A pdb=" N GLU Y 158 " --> pdb=" O LEU Y 154 " (cutoff:3.500A) Processing helix chain 'Y' and resid 252 through 256 Processing helix chain 'Y' and resid 309 through 311 No H-bonds generated for 'chain 'Y' and resid 309 through 311' Processing helix chain 'Y' and resid 447 through 451 Processing helix chain 'x' and resid 132 through 221 removed outlier: 4.129A pdb=" N UNK x 167 " --> pdb=" O UNK x 163 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 137 through 141 removed outlier: 7.130A pdb=" N VAL G 108 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N SER G 140 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU G 110 " --> pdb=" O SER G 140 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL G 12 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N THR G 111 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ILE G 14 " --> pdb=" O THR G 111 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 39 through 42 Processing sheet with id= C, first strand: chain 'G' and resid 330 through 332 removed outlier: 6.318A pdb=" N ILE G 298 " --> pdb=" O SER G 331 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL G 156 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER G 301 " --> pdb=" O VAL G 156 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU G 158 " --> pdb=" O SER G 301 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 240 through 242 Processing sheet with id= E, first strand: chain 'H' and resid 29 through 32 removed outlier: 3.677A pdb=" N PHE H 31 " --> pdb=" O CYS H 17 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL H 10 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU H 104 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASN H 12 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR H 106 " --> pdb=" O ASN H 12 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR H 133 " --> pdb=" O VAL H 103 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 52 through 54 removed outlier: 3.576A pdb=" N VAL H 35 " --> pdb=" O LYS H 68 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG H 37 " --> pdb=" O THR H 66 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 297 through 300 removed outlier: 6.745A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N SER H 300 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N MET H 153 " --> pdb=" O SER H 300 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE H 165 " --> pdb=" O GLY H 150 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL H 152 " --> pdb=" O VAL H 163 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 239 through 241 Processing sheet with id= I, first strand: chain 'I' and resid 137 through 141 removed outlier: 7.237A pdb=" N VAL I 108 " --> pdb=" O PHE I 138 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N SER I 140 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU I 110 " --> pdb=" O SER I 140 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL I 12 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N THR I 111 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ILE I 14 " --> pdb=" O THR I 111 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE I 21 " --> pdb=" O PHE I 35 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR I 33 " --> pdb=" O ALA I 23 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 39 through 42 Processing sheet with id= K, first strand: chain 'I' and resid 298 through 301 removed outlier: 6.231A pdb=" N VAL I 156 " --> pdb=" O VAL I 299 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N SER I 301 " --> pdb=" O VAL I 156 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU I 158 " --> pdb=" O SER I 301 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 240 through 242 Processing sheet with id= M, first strand: chain 'J' and resid 118 through 122 removed outlier: 7.429A pdb=" N VAL J 89 " --> pdb=" O LEU J 119 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ALA J 121 " --> pdb=" O VAL J 89 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL J 91 " --> pdb=" O ALA J 121 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL J 16 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ILE J 92 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE J 18 " --> pdb=" O ILE J 92 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'J' and resid 303 through 306 removed outlier: 6.508A pdb=" N MET J 137 " --> pdb=" O VAL J 304 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE J 306 " --> pdb=" O MET J 137 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU J 139 " --> pdb=" O ILE J 306 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL J 138 " --> pdb=" O LEU J 149 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'J' and resid 246 through 250 Processing sheet with id= P, first strand: chain 'U' and resid 23 through 25 removed outlier: 6.677A pdb=" N ILE U 41 " --> pdb=" O ARG U 24 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'U' and resid 88 through 90 removed outlier: 7.005A pdb=" N ASN U 105 " --> pdb=" O VAL U 89 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'U' and resid 141 through 143 Processing sheet with id= S, first strand: chain 'V' and resid 8 through 10 Processing sheet with id= T, first strand: chain 'V' and resid 15 through 17 Processing sheet with id= U, first strand: chain 'V' and resid 144 through 147 removed outlier: 3.623A pdb=" N GLY V 155 " --> pdb=" O VAL V 145 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N SER V 147 " --> pdb=" O PHE V 153 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N PHE V 153 " --> pdb=" O SER V 147 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'Y' and resid 84 through 86 Processing sheet with id= W, first strand: chain 'Y' and resid 330 through 333 Processing sheet with id= X, first strand: chain 'Y' and resid 423 through 431 Processing sheet with id= Y, first strand: chain 'Y' and resid 43 through 50 removed outlier: 3.702A pdb=" N SER Y 281 " --> pdb=" O GLU Y 45 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP Y 47 " --> pdb=" O LYS Y 279 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS Y 279 " --> pdb=" O ASP Y 47 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N HIS Y 49 " --> pdb=" O LEU Y 277 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU Y 277 " --> pdb=" O HIS Y 49 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Y' and resid 69 through 74 removed outlier: 4.298A pdb=" N LYS Y 274 " --> pdb=" O CYS Y 70 " (cutoff:3.500A) 747 hydrogen bonds defined for protein. 2097 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: 5.72 Time building geometry restraints manager: 8.18 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: 3716 1.33 - 1.45: 4525 1.45 - 1.58: 11434 1.58 - 1.70: 14 1.70 - 1.82: 145 Bond restraints: 19834 Sorted by residual: bond pdb=" C4 ADP G 800 " pdb=" C5 ADP G 800 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C4 ADP I 800 " pdb=" C5 ADP I 800 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C4 ADP J 800 " pdb=" C5 ADP J 800 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" N ILE Y 321 " pdb=" CA ILE Y 321 " ideal model delta sigma weight residual 1.456 1.496 -0.040 8.70e-03 1.32e+04 2.08e+01 bond pdb=" N VAL V 140 " pdb=" CA VAL V 140 " ideal model delta sigma weight residual 1.456 1.496 -0.040 8.70e-03 1.32e+04 2.07e+01 ... (remaining 19829 not shown) Histogram of bond angle deviations from ideal: 97.58 - 105.02: 526 105.02 - 112.46: 9691 112.46 - 119.89: 9116 119.89 - 127.33: 7541 127.33 - 134.76: 120 Bond angle restraints: 26994 Sorted by residual: angle pdb=" N PRO Y 438 " pdb=" CA PRO Y 438 " pdb=" CB PRO Y 438 " ideal model delta sigma weight residual 103.30 110.04 -6.74 8.00e-01 1.56e+00 7.09e+01 angle pdb=" PB ATP H 401 " pdb=" O3B ATP H 401 " pdb=" PG ATP H 401 " ideal model delta sigma weight residual 139.87 132.11 7.76 1.00e+00 1.00e+00 6.01e+01 angle pdb=" PA ATP H 401 " pdb=" O3A ATP H 401 " pdb=" PB ATP H 401 " ideal model delta sigma weight residual 136.83 129.79 7.04 1.00e+00 1.00e+00 4.96e+01 angle pdb=" N PRO Y 447 " pdb=" CA PRO Y 447 " pdb=" CB PRO Y 447 " ideal model delta sigma weight residual 103.25 110.16 -6.91 1.05e+00 9.07e-01 4.33e+01 angle pdb=" N PRO Y 441 " pdb=" CA PRO Y 441 " pdb=" CB PRO Y 441 " ideal model delta sigma weight residual 103.25 110.09 -6.84 1.05e+00 9.07e-01 4.24e+01 ... (remaining 26989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.85: 11703 30.85 - 61.70: 261 61.70 - 92.55: 8 92.55 - 123.39: 4 123.39 - 154.24: 2 Dihedral angle restraints: 11978 sinusoidal: 4301 harmonic: 7677 Sorted by residual: dihedral pdb=" C5' ADP G 800 " pdb=" O5' ADP G 800 " pdb=" PA ADP G 800 " pdb=" O2A ADP G 800 " ideal model delta sinusoidal sigma weight residual -60.00 94.25 -154.24 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" O1B ADP G 800 " pdb=" O3A ADP G 800 " pdb=" PB ADP G 800 " pdb=" PA ADP G 800 " ideal model delta sinusoidal sigma weight residual -60.00 71.57 -131.58 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" C5' ADP J 800 " pdb=" O5' ADP J 800 " pdb=" PA ADP J 800 " pdb=" O2A ADP J 800 " ideal model delta sinusoidal sigma weight residual -60.00 62.62 -122.62 1 2.00e+01 2.50e-03 3.69e+01 ... (remaining 11975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1149 0.047 - 0.093: 984 0.093 - 0.140: 666 0.140 - 0.186: 266 0.186 - 0.233: 65 Chirality restraints: 3130 Sorted by residual: chirality pdb=" CA VAL H 9 " pdb=" N VAL H 9 " pdb=" C VAL H 9 " pdb=" CB VAL H 9 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB VAL G 318 " pdb=" CA VAL G 318 " pdb=" CG1 VAL G 318 " pdb=" CG2 VAL G 318 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE G 185 " pdb=" N ILE G 185 " pdb=" C ILE G 185 " pdb=" CB ILE G 185 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 3127 not shown) Planarity restraints: 3494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 357 " 0.035 2.00e-02 2.50e+03 2.81e-02 1.97e+01 pdb=" CG TRP G 357 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP G 357 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP G 357 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP G 357 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP G 357 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP G 357 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 357 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 357 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP G 357 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP G 357 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C TRP G 357 " -0.043 2.00e-02 2.50e+03 pdb=" O TRP G 357 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL G 358 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 375 " 0.009 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C THR G 375 " -0.033 2.00e-02 2.50e+03 pdb=" O THR G 375 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE G 376 " 0.011 2.00e-02 2.50e+03 ... (remaining 3491 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 9 2.41 - 3.03: 9652 3.03 - 3.66: 29700 3.66 - 4.28: 41560 4.28 - 4.90: 70399 Nonbonded interactions: 151320 Sorted by model distance: nonbonded pdb=" NH2 ARG Y 37 " pdb="ZN ZN Y 501 " model vdw 1.790 2.310 nonbonded pdb=" O LEU G 267 " pdb=" NE2 HIS H 173 " model vdw 2.215 2.520 nonbonded pdb=" N ALA G 49 " pdb=" OH TYR I 148 " model vdw 2.235 2.520 nonbonded pdb=" O THR G 111 " pdb=" OG1 THR G 111 " model vdw 2.265 2.440 nonbonded pdb=" O GLY G 67 " pdb=" OD2 ASP I 287 " model vdw 2.308 3.040 ... (remaining 151315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 7 through 361 or (resid 362 and (name N or name CA or name \ C or name O or name CB )) or resid 363 or (resid 364 through 366 and (name N or \ name CA or name C or name O or name CB )) or resid 367 through 376 or resid 800 \ )) selection = chain 'I' } ncs_group { reference = chain 'S' selection = chain 'T' } ncs_group { reference = (chain 'X' and resid 132 through 223) selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.790 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 55.730 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.120 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 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 : 0.014 0.118 19834 Z= 0.902 Angle : 1.766 12.934 26994 Z= 1.285 Chirality : 0.087 0.233 3130 Planarity : 0.003 0.028 3494 Dihedral : 13.070 154.242 7008 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.70 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.14), residues: 2298 helix: -1.58 (0.16), residues: 669 sheet: -2.29 (0.28), residues: 283 loop : -2.37 (0.14), residues: 1346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 614 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 614 average time/residue: 0.3287 time to fit residues: 302.3735 Evaluate side-chains 338 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 2.159 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 203 optimal weight: 30.0000 chunk 78 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 235 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 297 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 HIS I 16 ASN I 91 GLN ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 GLN ** J 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 20 ASN ** V 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 162 GLN ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 254 GLN Y 306 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19834 Z= 0.224 Angle : 0.649 11.186 26994 Z= 0.326 Chirality : 0.043 0.203 3130 Planarity : 0.004 0.061 3494 Dihedral : 7.420 165.706 2867 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.82 % Rotamer: Outliers : 0.11 % Allowed : 3.24 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.16), residues: 2298 helix: 0.37 (0.19), residues: 698 sheet: -1.37 (0.26), residues: 334 loop : -1.80 (0.15), residues: 1266 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 388 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 390 average time/residue: 0.3136 time to fit residues: 190.6771 Evaluate side-chains 248 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 2.254 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 0.0980 chunk 72 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 160 optimal weight: 40.0000 chunk 64 optimal weight: 6.9990 chunk 235 optimal weight: 20.0000 chunk 254 optimal weight: 40.0000 chunk 209 optimal weight: 7.9990 chunk 233 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 189 optimal weight: 20.0000 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN G 142 GLN G 166 HIS ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 263 GLN H 371 HIS I 10 GLN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 379 ASN ** U 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 140 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 19834 Z= 0.334 Angle : 0.695 9.173 26994 Z= 0.347 Chirality : 0.043 0.271 3130 Planarity : 0.005 0.060 3494 Dihedral : 7.321 179.609 2867 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.09 % Favored : 94.82 % Rotamer: Outliers : 0.11 % Allowed : 4.80 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.17), residues: 2298 helix: 0.63 (0.19), residues: 710 sheet: -1.18 (0.26), residues: 339 loop : -1.25 (0.16), residues: 1249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 330 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 331 average time/residue: 0.3077 time to fit residues: 158.9331 Evaluate side-chains 221 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 2.689 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2665 time to fit residues: 3.5802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 8.9990 chunk 177 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 chunk 236 optimal weight: 20.0000 chunk 250 optimal weight: 20.0000 chunk 123 optimal weight: 0.9980 chunk 224 optimal weight: 30.0000 chunk 67 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 120 ASN ** G 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 HIS ** I 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 GLN J 178 GLN ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 344 HIS J 351 ASN ** U 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 19834 Z= 0.435 Angle : 0.772 13.402 26994 Z= 0.391 Chirality : 0.043 0.187 3130 Planarity : 0.005 0.052 3494 Dihedral : 7.436 175.212 2867 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.57 % Favored : 94.34 % Rotamer: Outliers : 0.11 % Allowed : 3.72 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.17), residues: 2298 helix: 0.09 (0.19), residues: 708 sheet: -1.25 (0.26), residues: 337 loop : -0.94 (0.17), residues: 1253 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 270 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 272 average time/residue: 0.3200 time to fit residues: 136.2869 Evaluate side-chains 173 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 3.194 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 20.0000 chunk 142 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 173 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 224 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 GLN J 365 GLN ** U 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 163 GLN V 60 HIS ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 81 HIS ** Y 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19834 Z= 0.200 Angle : 0.605 9.641 26994 Z= 0.299 Chirality : 0.042 0.209 3130 Planarity : 0.004 0.042 3494 Dihedral : 6.799 167.098 2867 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.27 % Favored : 94.65 % Rotamer: Outliers : 0.11 % Allowed : 2.21 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.17), residues: 2298 helix: 0.50 (0.19), residues: 712 sheet: -0.90 (0.28), residues: 314 loop : -0.77 (0.17), residues: 1272 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 287 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 289 average time/residue: 0.3126 time to fit residues: 139.5554 Evaluate side-chains 194 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 2.122 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2147 time to fit residues: 3.1440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 250 optimal weight: 20.0000 chunk 208 optimal weight: 20.0000 chunk 116 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 280 ASN H 354 GLN I 44 HIS I 65 HIS ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 HIS ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 HIS ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 19834 Z= 0.419 Angle : 0.756 14.092 26994 Z= 0.377 Chirality : 0.043 0.207 3130 Planarity : 0.005 0.086 3494 Dihedral : 7.008 162.781 2867 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 24.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.48 % Favored : 93.43 % Rotamer: Outliers : 0.05 % Allowed : 2.59 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.17), residues: 2298 helix: 0.08 (0.19), residues: 707 sheet: -1.29 (0.26), residues: 345 loop : -0.84 (0.17), residues: 1246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 241 time to evaluate : 2.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 242 average time/residue: 0.3061 time to fit residues: 116.7768 Evaluate side-chains 161 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 2.311 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 50.0000 chunk 28 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 141 optimal weight: 0.9980 chunk 210 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 156 optimal weight: 30.0000 chunk 152 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 HIS ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 GLN ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 HIS V 162 GLN ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 HIS ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19834 Z= 0.199 Angle : 0.628 10.144 26994 Z= 0.308 Chirality : 0.043 0.189 3130 Planarity : 0.005 0.092 3494 Dihedral : 6.526 153.248 2867 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.48 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.17), residues: 2298 helix: 0.41 (0.20), residues: 695 sheet: -0.93 (0.27), residues: 316 loop : -0.50 (0.18), residues: 1287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2873 time to fit residues: 114.9221 Evaluate side-chains 174 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.231 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 158 optimal weight: 20.0000 chunk 170 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 196 optimal weight: 5.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 HIS ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN I 65 HIS ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 HIS V 162 GLN ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.6171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19834 Z= 0.221 Angle : 0.625 10.298 26994 Z= 0.306 Chirality : 0.042 0.155 3130 Planarity : 0.004 0.053 3494 Dihedral : 6.410 152.713 2867 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.79 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2298 helix: 0.44 (0.20), residues: 695 sheet: -0.80 (0.28), residues: 317 loop : -0.44 (0.18), residues: 1286 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2974 time to fit residues: 115.4693 Evaluate side-chains 164 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 2.227 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 1.9990 chunk 239 optimal weight: 0.1980 chunk 218 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 210 optimal weight: 30.0000 chunk 220 optimal weight: 0.9990 chunk 231 optimal weight: 8.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN I 65 HIS ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 162 GLN ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.6331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19834 Z= 0.224 Angle : 0.627 10.911 26994 Z= 0.307 Chirality : 0.042 0.166 3130 Planarity : 0.004 0.055 3494 Dihedral : 6.286 146.637 2867 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.70 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 2298 helix: 0.54 (0.20), residues: 688 sheet: -0.74 (0.27), residues: 320 loop : -0.42 (0.18), residues: 1290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.2808 time to fit residues: 108.1693 Evaluate side-chains 162 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.425 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 3.9990 chunk 245 optimal weight: 8.9990 chunk 150 optimal weight: 0.0870 chunk 116 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 258 optimal weight: 30.0000 chunk 237 optimal weight: 20.0000 chunk 205 optimal weight: 40.0000 chunk 21 optimal weight: 8.9990 chunk 158 optimal weight: 20.0000 chunk 125 optimal weight: 0.0870 overall best weight: 3.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN I 65 HIS ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 97 GLN ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 162 GLN ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.6552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19834 Z= 0.271 Angle : 0.651 10.728 26994 Z= 0.320 Chirality : 0.042 0.151 3130 Planarity : 0.005 0.061 3494 Dihedral : 6.286 139.994 2867 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.35 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 2298 helix: 0.48 (0.20), residues: 697 sheet: -0.96 (0.27), residues: 337 loop : -0.44 (0.18), residues: 1264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2669 time to fit residues: 101.3308 Evaluate side-chains 157 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.046 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 10.0000 chunk 218 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 189 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 205 optimal weight: 40.0000 chunk 86 optimal weight: 0.9990 chunk 211 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN H 88 HIS H 280 ASN I 16 ASN I 65 HIS ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 297 ASN ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 162 GLN ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.046485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.031539 restraints weight = 128720.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.032879 restraints weight = 73330.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.033844 restraints weight = 48955.432| |-----------------------------------------------------------------------------| r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.6512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19834 Z= 0.173 Angle : 0.623 11.024 26994 Z= 0.301 Chirality : 0.042 0.159 3130 Planarity : 0.004 0.054 3494 Dihedral : 6.012 134.802 2867 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.13 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2298 helix: 0.55 (0.20), residues: 690 sheet: -0.61 (0.28), residues: 318 loop : -0.32 (0.18), residues: 1290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3757.91 seconds wall clock time: 69 minutes 47.80 seconds (4187.80 seconds total)