Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 19:42:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w98_21580/04_2023/6w98_21580_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w98_21580/04_2023/6w98_21580.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w98_21580/04_2023/6w98_21580_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w98_21580/04_2023/6w98_21580_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w98_21580/04_2023/6w98_21580_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w98_21580/04_2023/6w98_21580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w98_21580/04_2023/6w98_21580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w98_21580/04_2023/6w98_21580_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w98_21580/04_2023/6w98_21580_neut_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 2 5.49 5 S 22 5.16 5 C 6573 2.51 5 N 1810 2.21 5 O 1908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 37": "OD1" <-> "OD2" Residue "A ASP 41": "OD1" <-> "OD2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 434": "OD1" <-> "OD2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "A TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 608": "OD1" <-> "OD2" Residue "A ARG 652": "NH1" <-> "NH2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ASP 694": "OD1" <-> "OD2" Residue "A ARG 759": "NH1" <-> "NH2" Residue "A ARG 764": "NH1" <-> "NH2" Residue "A GLU 790": "OE1" <-> "OE2" Residue "A ASP 792": "OD1" <-> "OD2" Residue "A ASP 875": "OD1" <-> "OD2" Residue "A GLU 905": "OE1" <-> "OE2" Residue "A ARG 911": "NH1" <-> "NH2" Residue "A ARG 924": "NH1" <-> "NH2" Residue "A ARG 936": "NH1" <-> "NH2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A ASP 955": "OD1" <-> "OD2" Residue "A ARG 1027": "NH1" <-> "NH2" Residue "A ASP 1030": "OD1" <-> "OD2" Residue "A ASP 1034": "OD1" <-> "OD2" Residue "A ASP 1057": "OD1" <-> "OD2" Residue "A ARG 1061": "NH1" <-> "NH2" Residue "A PHE 1066": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1067": "OD1" <-> "OD2" Residue "A ASP 1140": "OD1" <-> "OD2" Residue "A ASP 1164": "OD1" <-> "OD2" Residue "A ARG 1204": "NH1" <-> "NH2" Residue "A ARG 1219": "NH1" <-> "NH2" Residue "A ARG 1389": "NH1" <-> "NH2" Residue "B GLU 5": "OE1" <-> "OE2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B ASP 70": "OD1" <-> "OD2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10317 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9653 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1312, 9643 Classifications: {'peptide': 1312} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1202} Chain breaks: 6 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 94 Conformer: "B" Number of residues, atoms: 1312, 9643 Classifications: {'peptide': 1312} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1202} Chain breaks: 6 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 94 bond proxies already assigned to first conformer: 9872 Chain: "B" Number of atoms: 605 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 77, 597 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 75} Conformer: "B" Number of residues, atoms: 77, 597 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 75} bond proxies already assigned to first conformer: 592 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 59 Unusual residues: {' CA': 2, '6OU': 1, 'PNS': 1} Classifications: {'undetermined': 4, 'water': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS A 550 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 550 " occ=0.50 residue: pdb=" N AASP B 56 " occ=0.60 ... (14 atoms not shown) pdb=" OD2BASP B 56 " occ=0.40 Time building chain proxies: 10.75, per 1000 atoms: 1.04 Number of scatterers: 10317 At special positions: 0 Unit cell: (143.168, 99.687, 95.445, 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) Ca 2 19.99 S 22 16.00 P 2 15.00 O 1908 8.00 N 1810 7.00 C 6573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 886 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A1104 " - pdb=" SG CYS A1139 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.15 Conformation dependent library (CDL) restraints added in 3.1 seconds 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2550 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 14 sheets defined 34.3% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 13 through 26 removed outlier: 3.576A pdb=" N VAL A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 No H-bonds generated for 'chain 'A' and resid 41 through 44' Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.588A pdb=" N ALA A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 91 through 117 removed outlier: 3.616A pdb=" N VAL A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 136 through 142 removed outlier: 3.834A pdb=" N THR A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 166 Proline residue: A 156 - end of helix removed outlier: 3.518A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 172 through 185 removed outlier: 3.630A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 212 through 242 removed outlier: 3.996A pdb=" N TRP A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix removed outlier: 5.928A pdb=" N TRP A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TRP A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA A 235 " --> pdb=" O TRP A 231 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 262 through 267 Processing helix chain 'A' and resid 289 through 307 removed outlier: 3.502A pdb=" N VAL A 293 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 327 removed outlier: 3.501A pdb=" N VAL A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 363 through 377 removed outlier: 3.641A pdb=" N LEU A 368 " --> pdb=" O PRO A 364 " (cutoff:3.500A) Proline residue: A 369 - end of helix removed outlier: 3.542A pdb=" N HIS A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 418 removed outlier: 3.553A pdb=" N ILE A 409 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 410 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 413 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 415 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 417 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 418 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 423 No H-bonds generated for 'chain 'A' and resid 420 through 423' Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 476 through 480 Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.808A pdb=" N SER A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 524 removed outlier: 3.556A pdb=" N ARG A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 554 removed outlier: 3.695A pdb=" N HIS A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 619 through 631 removed outlier: 4.078A pdb=" N LEU A 622 " --> pdb=" O PRO A 619 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 623 " --> pdb=" O GLU A 620 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 624 " --> pdb=" O ALA A 621 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 625 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN A 626 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 628 " --> pdb=" O LEU A 625 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 629 " --> pdb=" O ASN A 626 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 631 " --> pdb=" O ARG A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 647 Processing helix chain 'A' and resid 729 through 731 No H-bonds generated for 'chain 'A' and resid 729 through 731' Processing helix chain 'A' and resid 733 through 736 removed outlier: 3.737A pdb=" N ALA A 736 " --> pdb=" O THR A 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 733 through 736' Processing helix chain 'A' and resid 935 through 939 Processing helix chain 'A' and resid 960 through 963 Processing helix chain 'A' and resid 1092 through 1095 No H-bonds generated for 'chain 'A' and resid 1092 through 1095' Processing helix chain 'A' and resid 1125 through 1129 Processing helix chain 'A' and resid 1231 through 1233 No H-bonds generated for 'chain 'A' and resid 1231 through 1233' Processing helix chain 'A' and resid 1255 through 1266 Processing helix chain 'A' and resid 1269 through 1277 Processing helix chain 'A' and resid 1296 through 1309 removed outlier: 3.542A pdb=" N VAL A1300 " --> pdb=" O PRO A1296 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A1301 " --> pdb=" O ALA A1297 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A1303 " --> pdb=" O GLY A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1327 removed outlier: 3.636A pdb=" N VAL A1326 " --> pdb=" O LEU A1322 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP A1327 " --> pdb=" O ALA A1323 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1355 removed outlier: 3.689A pdb=" N THR A1336 " --> pdb=" O LEU A1332 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY A1339 " --> pdb=" O VAL A1335 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A1340 " --> pdb=" O THR A1336 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A1341 " --> pdb=" O ALA A1337 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A1346 " --> pdb=" O LEU A1342 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A1347 " --> pdb=" O ALA A1343 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A1354 " --> pdb=" O ALA A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1386 removed outlier: 3.663A pdb=" N GLN A1373 " --> pdb=" O SER A1369 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A1377 " --> pdb=" O GLN A1373 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A1378 " --> pdb=" O LEU A1374 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER A1379 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A1386 " --> pdb=" O SER A1382 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 15 Processing helix chain 'B' and resid 19 through 21 No H-bonds generated for 'chain 'B' and resid 19 through 21' Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 56 through 61 removed outlier: 4.320A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 74 removed outlier: 3.784A pdb=" N TYR B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 455 through 459 removed outlier: 7.439A pdb=" N LEU A 457 " --> pdb=" O SER A 528 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU A 530 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 459 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL A 532 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 563 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA A 594 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LYS A 561 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 577 through 579 removed outlier: 6.604A pdb=" N ILE A1059 " --> pdb=" O VAL A 578 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 605 through 608 removed outlier: 3.663A pdb=" N GLN A1236 " --> pdb=" O VAL A1208 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR A1227 " --> pdb=" O VAL A1239 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 613 through 615 Processing sheet with id= E, first strand: chain 'A' and resid 657 through 659 removed outlier: 6.761A pdb=" N GLY A 873 " --> pdb=" O VAL A 658 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP A 926 " --> pdb=" O ASP A1164 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL A1166 " --> pdb=" O ARG A 924 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG A 924 " --> pdb=" O VAL A1166 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU A1168 " --> pdb=" O THR A 922 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N THR A 922 " --> pdb=" O LEU A1168 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU A 925 " --> pdb=" O ALA A1136 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 704 through 708 removed outlier: 3.756A pdb=" N ASN A 704 " --> pdb=" O THR A 861 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE A 910 " --> pdb=" O HIS A 858 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA A 860 " --> pdb=" O ILE A 910 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 914 " --> pdb=" O VAL A 862 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 710 through 714 removed outlier: 3.858A pdb=" N GLY A 794 " --> pdb=" O THR A 791 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 806 through 810 removed outlier: 3.754A pdb=" N GLU A 839 " --> pdb=" O THR A 774 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU A 842 " --> pdb=" O VAL A 854 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 919 through 921 Processing sheet with id= J, first strand: chain 'A' and resid 946 through 948 Processing sheet with id= K, first strand: chain 'A' and resid 995 through 997 removed outlier: 3.768A pdb=" N THR A 995 " --> pdb=" O THR A1045 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1036 through 1039 removed outlier: 3.781A pdb=" N THR A1036 " --> pdb=" O LEU A1002 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A1002 " --> pdb=" O THR A1036 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA A 999 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1099 through 1102 Processing sheet with id= N, first strand: chain 'A' and resid 1192 through 1197 356 hydrogen bonds defined for protein. 990 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: 4.14 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1695 1.30 - 1.43: 2619 1.43 - 1.56: 6208 1.56 - 1.69: 3 1.69 - 1.81: 35 Bond restraints: 10560 Sorted by residual: bond pdb=" C16 6OU A2003 " pdb=" O18 6OU A2003 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C31 6OU A2003 " pdb=" O30 6OU A2003 " ideal model delta sigma weight residual 1.331 1.404 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C THR A1132 " pdb=" N VAL A1133 " ideal model delta sigma weight residual 1.334 1.307 0.026 1.24e-02 6.50e+03 4.53e+00 bond pdb=" CB THR A 791 " pdb=" CG2 THR A 791 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.08e+00 bond pdb=" CA LEU A1168 " pdb=" CB LEU A1168 " ideal model delta sigma weight residual 1.531 1.474 0.057 3.28e-02 9.30e+02 3.04e+00 ... (remaining 10555 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.76: 357 105.76 - 112.84: 5822 112.84 - 119.92: 3502 119.92 - 127.00: 4601 127.00 - 134.08: 218 Bond angle restraints: 14500 Sorted by residual: angle pdb=" O22 6OU A2003 " pdb=" P23 6OU A2003 " pdb=" O26 6OU A2003 " ideal model delta sigma weight residual 93.95 109.17 -15.22 3.00e+00 1.11e-01 2.57e+01 angle pdb=" N GLY A 836 " pdb=" CA GLY A 836 " pdb=" C GLY A 836 " ideal model delta sigma weight residual 110.90 116.21 -5.31 1.53e+00 4.27e-01 1.20e+01 angle pdb=" O24 6OU A2003 " pdb=" P23 6OU A2003 " pdb=" O25 6OU A2003 " ideal model delta sigma weight residual 118.72 109.03 9.69 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C33 6OU A2003 " pdb=" C31 6OU A2003 " pdb=" O30 6OU A2003 " ideal model delta sigma weight residual 111.22 120.78 -9.56 3.00e+00 1.11e-01 1.01e+01 angle pdb=" C15 6OU A2003 " pdb=" C16 6OU A2003 " pdb=" O18 6OU A2003 " ideal model delta sigma weight residual 110.70 120.21 -9.51 3.00e+00 1.11e-01 1.01e+01 ... (remaining 14495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.83: 5886 19.83 - 39.67: 328 39.67 - 59.50: 38 59.50 - 79.33: 13 79.33 - 99.16: 2 Dihedral angle restraints: 6267 sinusoidal: 2317 harmonic: 3950 Sorted by residual: dihedral pdb=" CA PRO A1010 " pdb=" C PRO A1010 " pdb=" N ALA A1011 " pdb=" CA ALA A1011 " ideal model delta harmonic sigma weight residual -180.00 -153.60 -26.40 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ASP A 977 " pdb=" C ASP A 977 " pdb=" N SER A 978 " pdb=" CA SER A 978 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA PRO A 653 " pdb=" C PRO A 653 " pdb=" N GLY A 654 " pdb=" CA GLY A 654 " ideal model delta harmonic sigma weight residual 180.00 157.41 22.59 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 6264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 791 0.030 - 0.060: 534 0.060 - 0.090: 237 0.090 - 0.120: 128 0.120 - 0.150: 32 Chirality restraints: 1722 Sorted by residual: chirality pdb=" CA THR A 661 " pdb=" N THR A 661 " pdb=" C THR A 661 " pdb=" CB THR A 661 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA PRO A 62 " pdb=" N PRO A 62 " pdb=" C PRO A 62 " pdb=" CB PRO A 62 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA VAL A1208 " pdb=" N VAL A1208 " pdb=" C VAL A1208 " pdb=" CB VAL A1208 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 1719 not shown) Planarity restraints: 1875 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 974 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO A 975 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 155 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A 156 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 156 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 156 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 222 " 0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO A 223 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " 0.029 5.00e-02 4.00e+02 ... (remaining 1872 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 87 2.57 - 3.15: 8187 3.15 - 3.74: 15513 3.74 - 4.32: 21938 4.32 - 4.90: 37495 Nonbonded interactions: 83220 Sorted by model distance: nonbonded pdb=" O ALA A 735 " pdb=" OD1 ASP A 738 " model vdw 1.990 3.040 nonbonded pdb=" OD2 ASP A 965 " pdb=" OG1 THR A 970 " model vdw 2.077 2.440 nonbonded pdb=" O ALA A 735 " pdb="CA CA A2001 " model vdw 2.107 2.510 nonbonded pdb=" O ALA A1075 " pdb="CA CA A2002 " model vdw 2.159 2.510 nonbonded pdb=" O ALA A 962 " pdb="CA CA A2002 " model vdw 2.183 2.510 ... (remaining 83215 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=0.40 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: 1.210 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: 0.000 Extract box with map and model: 6.060 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 37.330 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.010 0.077 10560 Z= 0.657 Angle : 0.864 15.215 14500 Z= 0.431 Chirality : 0.051 0.150 1722 Planarity : 0.007 0.056 1875 Dihedral : 12.852 99.163 3711 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.37 % Favored : 95.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -4.30 (0.17), residues: 1379 helix: -4.11 (0.12), residues: 481 sheet: -1.60 (0.31), residues: 204 loop : -2.21 (0.19), residues: 694 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.213 Fit side-chains 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: 171 average time/residue: 1.2382 time to fit residues: 227.8594 Evaluate side-chains 99 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 58 optimal weight: 0.0970 chunk 35 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 0.0770 chunk 125 optimal weight: 3.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 360 HIS A1068 GLN A1151 GLN B 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10560 Z= 0.192 Angle : 0.637 7.995 14500 Z= 0.316 Chirality : 0.044 0.271 1722 Planarity : 0.006 0.050 1875 Dihedral : 6.736 83.627 1508 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -2.72 (0.19), residues: 1379 helix: -2.28 (0.19), residues: 475 sheet: -0.92 (0.32), residues: 209 loop : -1.65 (0.21), residues: 695 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 124 average time/residue: 1.0735 time to fit residues: 145.6603 Evaluate side-chains 99 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.1044 time to fit residues: 1.9628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 chunk 100 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.059 10560 Z= 0.489 Angle : 0.724 8.928 14500 Z= 0.354 Chirality : 0.049 0.304 1722 Planarity : 0.006 0.052 1875 Dihedral : 6.838 81.378 1508 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.73 % Favored : 95.19 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -1.97 (0.20), residues: 1379 helix: -1.17 (0.21), residues: 489 sheet: -0.74 (0.32), residues: 218 loop : -1.54 (0.21), residues: 672 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 98 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 14 residues processed: 114 average time/residue: 1.0469 time to fit residues: 131.5476 Evaluate side-chains 103 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 1.299 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 6 average time/residue: 0.6023 time to fit residues: 6.3215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.1980 chunk 94 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 125 optimal weight: 0.2980 chunk 133 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 648 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 10560 Z= 0.197 Angle : 0.601 9.159 14500 Z= 0.289 Chirality : 0.043 0.279 1722 Planarity : 0.005 0.048 1875 Dihedral : 6.352 73.407 1508 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -1.29 (0.21), residues: 1379 helix: -0.43 (0.23), residues: 480 sheet: -0.45 (0.34), residues: 213 loop : -1.25 (0.22), residues: 686 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 14 residues processed: 130 average time/residue: 1.0306 time to fit residues: 146.8913 Evaluate side-chains 111 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.1547 time to fit residues: 2.2779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 30.0000 chunk 0 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 983 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.051 10560 Z= 0.469 Angle : 0.693 9.008 14500 Z= 0.337 Chirality : 0.048 0.316 1722 Planarity : 0.005 0.050 1875 Dihedral : 6.597 72.471 1508 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.95 % Favored : 94.97 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -1.23 (0.21), residues: 1379 helix: -0.30 (0.23), residues: 484 sheet: -0.53 (0.33), residues: 219 loop : -1.24 (0.22), residues: 676 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 18 residues processed: 106 average time/residue: 1.0538 time to fit residues: 123.5595 Evaluate side-chains 104 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 5 average time/residue: 0.1556 time to fit residues: 2.8172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 0.0980 chunk 32 optimal weight: 0.8980 chunk 133 optimal weight: 20.0000 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 70 optimal weight: 0.7980 chunk 128 optimal weight: 7.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 983 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10560 Z= 0.183 Angle : 0.580 9.340 14500 Z= 0.278 Chirality : 0.043 0.287 1722 Planarity : 0.005 0.049 1875 Dihedral : 6.148 73.331 1508 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.79 (0.22), residues: 1379 helix: 0.19 (0.24), residues: 483 sheet: -0.32 (0.33), residues: 218 loop : -1.07 (0.23), residues: 678 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 19 residues processed: 124 average time/residue: 0.9485 time to fit residues: 130.0861 Evaluate side-chains 116 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 14 residues processed: 5 average time/residue: 0.5286 time to fit residues: 4.6574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 133 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 81 optimal weight: 0.0030 chunk 61 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 HIS A 768 ASN ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10560 Z= 0.196 Angle : 0.589 11.666 14500 Z= 0.280 Chirality : 0.043 0.313 1722 Planarity : 0.005 0.050 1875 Dihedral : 5.967 74.092 1508 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.52 (0.22), residues: 1379 helix: 0.48 (0.25), residues: 481 sheet: -0.17 (0.34), residues: 218 loop : -0.97 (0.23), residues: 680 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 19 residues processed: 118 average time/residue: 0.9799 time to fit residues: 127.8125 Evaluate side-chains 114 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 4 average time/residue: 0.1645 time to fit residues: 2.6257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 0.0770 chunk 84 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 768 ASN ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 10560 Z= 0.242 Angle : 0.610 10.176 14500 Z= 0.290 Chirality : 0.044 0.336 1722 Planarity : 0.005 0.059 1875 Dihedral : 5.945 74.329 1508 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 (0.22), residues: 1379 helix: 0.53 (0.25), residues: 483 sheet: -0.14 (0.34), residues: 218 loop : -0.98 (0.23), residues: 678 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 18 residues processed: 119 average time/residue: 1.0100 time to fit residues: 132.1060 Evaluate side-chains 114 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 1.038 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.1312 time to fit residues: 2.1846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 74 optimal weight: 0.3980 chunk 53 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 0.0020 chunk 131 optimal weight: 9.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 ASN ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10560 Z= 0.185 Angle : 0.583 9.176 14500 Z= 0.277 Chirality : 0.043 0.319 1722 Planarity : 0.005 0.065 1875 Dihedral : 5.771 74.999 1508 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.35 (0.22), residues: 1379 helix: 0.64 (0.25), residues: 484 sheet: -0.06 (0.35), residues: 218 loop : -0.89 (0.23), residues: 677 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 115 average time/residue: 1.0354 time to fit residues: 131.4244 Evaluate side-chains 110 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 1.155 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.1642 time to fit residues: 1.8246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.0970 chunk 62 optimal weight: 0.0470 chunk 91 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 0.0470 chunk 86 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 77 HIS ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 ASN ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 10560 Z= 0.159 Angle : 0.577 11.214 14500 Z= 0.273 Chirality : 0.043 0.316 1722 Planarity : 0.005 0.060 1875 Dihedral : 5.590 75.981 1508 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.15 (0.23), residues: 1379 helix: 0.84 (0.25), residues: 482 sheet: 0.02 (0.35), residues: 218 loop : -0.78 (0.23), residues: 679 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 119 average time/residue: 0.9695 time to fit residues: 127.9705 Evaluate side-chains 114 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 1.169 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.2628 time to fit residues: 1.9442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 0.0570 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.0770 chunk 96 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 77 HIS ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 ASN ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.129622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.094593 restraints weight = 32049.376| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.60 r_work: 0.2874 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 10560 Z= 0.172 Angle : 0.579 11.777 14500 Z= 0.275 Chirality : 0.043 0.338 1722 Planarity : 0.005 0.063 1875 Dihedral : 5.505 76.680 1508 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.06 (0.23), residues: 1379 helix: 0.93 (0.25), residues: 481 sheet: 0.05 (0.35), residues: 218 loop : -0.74 (0.23), residues: 680 =============================================================================== Job complete usr+sys time: 3368.76 seconds wall clock time: 60 minutes 43.34 seconds (3643.34 seconds total)