Starting phenix.real_space_refine on Fri Mar 15 03:11:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w98_21580/03_2024/6w98_21580_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w98_21580/03_2024/6w98_21580.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w98_21580/03_2024/6w98_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_21580/03_2024/6w98_21580_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w98_21580/03_2024/6w98_21580_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w98_21580/03_2024/6w98_21580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w98_21580/03_2024/6w98_21580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w98_21580/03_2024/6w98_21580_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w98_21580/03_2024/6w98_21580_neut_updated.pdb" } resolution = 2.9 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= 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 11.21, per 1000 atoms: 1.09 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: 3.95 Conformation dependent library (CDL) restraints added in 3.5 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: 3.22 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: 3.95 Time building geometry restraints manager: 4.31 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 - 27.44: 6089 27.44 - 54.88: 168 54.88 - 82.32: 18 82.32 - 109.75: 2 109.75 - 137.19: 3 Dihedral angle restraints: 6280 sinusoidal: 2330 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 6277 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: 1.040 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.560 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 39.250 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.190 ------------------------------------------------------------------------------- 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 : 13.563 137.191 3724 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 % Allowed : 1.62 % Favored : 98.38 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 232 HIS 0.010 0.002 HIS A 675 PHE 0.018 0.002 PHE A 433 TYR 0.016 0.002 TYR A 439 ARG 0.011 0.001 ARG A 764 *********************** 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 : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 ARG cc_start: 0.7992 (ttt90) cc_final: 0.7677 (tpm170) REVERT: A 689 PHE cc_start: 0.8948 (m-80) cc_final: 0.8740 (m-80) REVERT: A 953 VAL cc_start: 0.6943 (m) cc_final: 0.6629 (p) REVERT: A 959 SER cc_start: 0.7810 (p) cc_final: 0.7502 (m) REVERT: A 1014 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8321 (mtpm) REVERT: A 1210 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8338 (mt-10) REVERT: B 4 GLU cc_start: 0.8513 (mp0) cc_final: 0.7864 (mm-30) REVERT: B 44 MET cc_start: 0.7042 (mtm) cc_final: 0.5921 (mtp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 1.1487 time to fit residues: 211.7663 Evaluate side-chains 103 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 A 690 ASN A1068 GLN A1151 GLN B 73 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10560 Z= 0.198 Angle : 0.633 7.992 14500 Z= 0.316 Chirality : 0.044 0.270 1722 Planarity : 0.006 0.049 1875 Dihedral : 8.679 119.137 1521 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.34 % Allowed : 9.64 % Favored : 89.03 % 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: -2.77 (0.19), residues: 1379 helix: -2.21 (0.19), residues: 483 sheet: -0.96 (0.32), residues: 209 loop : -1.76 (0.20), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 214 HIS 0.003 0.001 HIS A 675 PHE 0.010 0.001 PHE B 50 TYR 0.014 0.001 TYR A 439 ARG 0.008 0.001 ARG A 267 *********************** 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 130 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ARG cc_start: 0.8603 (tpp-160) cc_final: 0.8082 (mmt90) REVERT: A 844 GLN cc_start: 0.8288 (tt0) cc_final: 0.8008 (tt0) REVERT: A 953 VAL cc_start: 0.6951 (m) cc_final: 0.6643 (p) REVERT: A 959 SER cc_start: 0.7854 (p) cc_final: 0.7477 (m) REVERT: A 1198 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7466 (pm20) outliers start: 14 outliers final: 5 residues processed: 123 average time/residue: 1.0174 time to fit residues: 137.2937 Evaluate side-chains 102 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1377 LEU 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: 0.6980 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 42 optimal weight: 0.0270 chunk 100 optimal weight: 0.6980 overall best weight: 0.8840 ------------------------------------------------------------------------------- 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: 0.8137 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10560 Z= 0.250 Angle : 0.604 7.862 14500 Z= 0.294 Chirality : 0.044 0.284 1722 Planarity : 0.005 0.048 1875 Dihedral : 7.916 94.163 1521 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.93 % Favored : 95.99 % Rotamer: Outliers : 1.91 % Allowed : 10.11 % Favored : 87.98 % 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: -1.70 (0.21), residues: 1379 helix: -0.94 (0.22), residues: 482 sheet: -0.52 (0.34), residues: 210 loop : -1.39 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 214 HIS 0.005 0.001 HIS A 675 PHE 0.008 0.001 PHE A 433 TYR 0.014 0.001 TYR A 439 ARG 0.007 0.000 ARG A 764 *********************** 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 125 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 767 THR cc_start: 0.8015 (p) cc_final: 0.7601 (t) REVERT: A 844 GLN cc_start: 0.8269 (tt0) cc_final: 0.7948 (tt0) REVERT: A 959 SER cc_start: 0.8008 (p) cc_final: 0.7591 (m) REVERT: A 1198 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7538 (pm20) REVERT: B 44 MET cc_start: 0.7073 (mmp) cc_final: 0.6550 (mtp) outliers start: 20 outliers final: 12 residues processed: 112 average time/residue: 0.9549 time to fit residues: 117.8596 Evaluate side-chains 106 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1377 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 6.9990 chunk 94 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 0.0870 chunk 59 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 125 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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: 0.8119 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10560 Z= 0.177 Angle : 0.562 8.990 14500 Z= 0.270 Chirality : 0.043 0.299 1722 Planarity : 0.005 0.048 1875 Dihedral : 7.411 80.991 1521 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.29 % Allowed : 10.78 % Favored : 86.93 % 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: -1.08 (0.21), residues: 1379 helix: -0.24 (0.23), residues: 482 sheet: -0.23 (0.34), residues: 210 loop : -1.17 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 214 HIS 0.003 0.001 HIS A 675 PHE 0.008 0.001 PHE A 433 TYR 0.012 0.001 TYR A 439 ARG 0.009 0.000 ARG A 764 *********************** 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 143 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.7566 (mpt180) REVERT: A 371 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8760 (mm) REVERT: A 426 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7878 (mtp180) REVERT: A 767 THR cc_start: 0.8020 (p) cc_final: 0.7648 (t) REVERT: A 844 GLN cc_start: 0.8213 (tt0) cc_final: 0.7921 (tt0) REVERT: A 959 SER cc_start: 0.7955 (p) cc_final: 0.7538 (m) REVERT: B 44 MET cc_start: 0.7342 (mmp) cc_final: 0.6636 (mtp) outliers start: 24 outliers final: 10 residues processed: 132 average time/residue: 0.9532 time to fit residues: 138.3959 Evaluate side-chains 117 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1077 VAL 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: 0.7980 chunk 55 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8148 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10560 Z= 0.265 Angle : 0.602 8.144 14500 Z= 0.288 Chirality : 0.044 0.330 1722 Planarity : 0.005 0.048 1875 Dihedral : 7.017 76.770 1521 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.58 % Allowed : 12.12 % Favored : 85.31 % 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: -0.91 (0.22), residues: 1379 helix: -0.02 (0.24), residues: 489 sheet: -0.24 (0.34), residues: 213 loop : -1.10 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 232 HIS 0.009 0.001 HIS A 360 PHE 0.009 0.001 PHE A 107 TYR 0.015 0.001 TYR A 439 ARG 0.010 0.000 ARG A 764 *********************** 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 135 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8498 (mtm-85) cc_final: 0.7589 (mpt180) REVERT: A 147 SER cc_start: 0.8245 (OUTLIER) cc_final: 0.7797 (p) REVERT: A 371 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8806 (mm) REVERT: A 648 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8397 (tp-100) REVERT: A 767 THR cc_start: 0.8052 (p) cc_final: 0.7623 (t) REVERT: A 844 GLN cc_start: 0.8341 (tt0) cc_final: 0.8017 (tt0) REVERT: A 935 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8583 (tt) REVERT: A 959 SER cc_start: 0.7913 (p) cc_final: 0.7532 (m) REVERT: A 983 HIS cc_start: 0.6792 (t-170) cc_final: 0.6565 (p90) REVERT: A 1097 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8543 (mtmm) REVERT: B 44 MET cc_start: 0.7507 (mmp) cc_final: 0.6987 (mtt) outliers start: 27 outliers final: 14 residues processed: 126 average time/residue: 0.9447 time to fit residues: 131.8974 Evaluate side-chains 117 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1001 ARG Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1097 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 78 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 128 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10560 Z= 0.198 Angle : 0.572 8.904 14500 Z= 0.274 Chirality : 0.043 0.321 1722 Planarity : 0.005 0.052 1875 Dihedral : 6.575 83.981 1521 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.39 % Allowed : 12.79 % Favored : 84.83 % 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: -0.62 (0.22), residues: 1379 helix: 0.32 (0.24), residues: 483 sheet: -0.15 (0.34), residues: 213 loop : -0.99 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 232 HIS 0.007 0.001 HIS A 360 PHE 0.008 0.001 PHE A 107 TYR 0.013 0.001 TYR A 439 ARG 0.012 0.000 ARG A 764 *********************** 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 131 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8480 (mtm-85) cc_final: 0.7597 (mpt180) REVERT: A 147 SER cc_start: 0.8188 (OUTLIER) cc_final: 0.7759 (p) REVERT: A 371 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8802 (mm) REVERT: A 648 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8489 (tp-100) REVERT: A 767 THR cc_start: 0.8063 (p) cc_final: 0.7638 (t) REVERT: A 844 GLN cc_start: 0.8355 (tt0) cc_final: 0.7982 (tt0) REVERT: A 935 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8601 (tt) REVERT: A 959 SER cc_start: 0.7874 (p) cc_final: 0.7481 (m) REVERT: A 1097 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8539 (mtmm) REVERT: B 44 MET cc_start: 0.7568 (mmp) cc_final: 0.7035 (mtt) outliers start: 25 outliers final: 14 residues processed: 123 average time/residue: 0.9859 time to fit residues: 133.7235 Evaluate side-chains 123 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1097 LYS Chi-restraints excluded: chain A residue 1375 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.0020 chunk 76 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 0.0670 chunk 133 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.5528 ------------------------------------------------------------------------------- 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 983 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10560 Z= 0.180 Angle : 0.564 8.423 14500 Z= 0.269 Chirality : 0.043 0.325 1722 Planarity : 0.005 0.052 1875 Dihedral : 6.393 85.901 1521 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.19 % Allowed : 13.26 % Favored : 84.54 % 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: -0.41 (0.22), residues: 1379 helix: 0.53 (0.24), residues: 485 sheet: -0.05 (0.35), residues: 213 loop : -0.88 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 232 HIS 0.008 0.001 HIS A 360 PHE 0.007 0.001 PHE A 107 TYR 0.013 0.001 TYR A 439 ARG 0.013 0.000 ARG A 764 *********************** 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 135 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8455 (mtm-85) cc_final: 0.7667 (mmt180) REVERT: A 147 SER cc_start: 0.8100 (OUTLIER) cc_final: 0.7701 (p) REVERT: A 212 ARG cc_start: 0.7746 (ttt90) cc_final: 0.7424 (tpm170) REVERT: A 371 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8799 (mm) REVERT: A 523 ARG cc_start: 0.8460 (ttm-80) cc_final: 0.8236 (ttm110) REVERT: A 767 THR cc_start: 0.8075 (p) cc_final: 0.7649 (t) REVERT: A 768 ASN cc_start: 0.8354 (m110) cc_final: 0.8149 (m110) REVERT: A 844 GLN cc_start: 0.8321 (tt0) cc_final: 0.8031 (tt0) REVERT: A 935 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8570 (tt) REVERT: A 959 SER cc_start: 0.7942 (p) cc_final: 0.7478 (m) REVERT: A 1097 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8558 (mtmm) REVERT: B 44 MET cc_start: 0.7595 (mmp) cc_final: 0.7011 (mtt) outliers start: 23 outliers final: 14 residues processed: 127 average time/residue: 0.9573 time to fit residues: 133.7713 Evaluate side-chains 122 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1097 LYS Chi-restraints excluded: chain A residue 1354 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.0050 chunk 79 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 65 optimal weight: 0.0670 chunk 12 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 overall best weight: 0.4934 ------------------------------------------------------------------------------- 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 551 HIS A 648 GLN A 983 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10560 Z= 0.170 Angle : 0.565 8.947 14500 Z= 0.270 Chirality : 0.043 0.330 1722 Planarity : 0.005 0.057 1875 Dihedral : 6.245 88.154 1521 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.29 % Allowed : 13.65 % Favored : 84.06 % 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: -0.25 (0.22), residues: 1379 helix: 0.69 (0.24), residues: 482 sheet: 0.04 (0.35), residues: 213 loop : -0.80 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 232 HIS 0.006 0.001 HIS A 360 PHE 0.006 0.001 PHE A 107 TYR 0.013 0.001 TYR A 439 ARG 0.015 0.000 ARG A 764 *********************** 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 136 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8448 (mtm-85) cc_final: 0.7612 (tpt170) REVERT: A 147 SER cc_start: 0.8060 (OUTLIER) cc_final: 0.7680 (p) REVERT: A 212 ARG cc_start: 0.7748 (ttt90) cc_final: 0.7424 (tpm170) REVERT: A 371 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8788 (mm) REVERT: A 523 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.8217 (ttm110) REVERT: A 648 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8108 (tp40) REVERT: A 767 THR cc_start: 0.8082 (p) cc_final: 0.7649 (t) REVERT: A 768 ASN cc_start: 0.8355 (m110) cc_final: 0.8149 (m110) REVERT: A 844 GLN cc_start: 0.8298 (tt0) cc_final: 0.8003 (tt0) REVERT: A 954 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7748 (pp) REVERT: A 959 SER cc_start: 0.7945 (p) cc_final: 0.7487 (m) REVERT: A 1097 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8561 (mtmm) REVERT: B 44 MET cc_start: 0.7622 (mmp) cc_final: 0.7002 (mtt) outliers start: 24 outliers final: 15 residues processed: 127 average time/residue: 0.8990 time to fit residues: 126.0960 Evaluate side-chains 127 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1097 LYS Chi-restraints excluded: chain A residue 1354 LEU Chi-restraints excluded: chain A residue 1383 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 74 optimal weight: 0.0980 chunk 53 optimal weight: 0.0020 chunk 97 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- 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 983 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10560 Z= 0.221 Angle : 0.590 10.385 14500 Z= 0.280 Chirality : 0.044 0.342 1722 Planarity : 0.005 0.064 1875 Dihedral : 6.197 89.552 1521 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.29 % Allowed : 13.74 % Favored : 83.97 % 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: -0.21 (0.22), residues: 1379 helix: 0.71 (0.24), residues: 482 sheet: 0.06 (0.35), residues: 213 loop : -0.78 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 232 HIS 0.005 0.001 HIS A 983 PHE 0.008 0.001 PHE A 107 TYR 0.014 0.001 TYR A 439 ARG 0.014 0.000 ARG A 764 *********************** 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 130 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8459 (mtm-85) cc_final: 0.7622 (tpt170) REVERT: A 147 SER cc_start: 0.8151 (OUTLIER) cc_final: 0.7731 (p) REVERT: A 523 ARG cc_start: 0.8454 (ttm-80) cc_final: 0.8215 (ttm110) REVERT: A 767 THR cc_start: 0.8093 (p) cc_final: 0.7662 (t) REVERT: A 768 ASN cc_start: 0.8357 (m110) cc_final: 0.8143 (m110) REVERT: A 844 GLN cc_start: 0.8315 (tt0) cc_final: 0.8029 (tt0) REVERT: A 954 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7789 (pp) REVERT: A 959 SER cc_start: 0.7985 (p) cc_final: 0.7525 (m) REVERT: A 1097 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8569 (mtmm) REVERT: B 44 MET cc_start: 0.7631 (mmp) cc_final: 0.6994 (mtt) outliers start: 24 outliers final: 16 residues processed: 120 average time/residue: 0.9516 time to fit residues: 126.2143 Evaluate side-chains 123 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1097 LYS Chi-restraints excluded: chain A residue 1354 LEU Chi-restraints excluded: chain A residue 1383 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 0.0870 chunk 91 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 0.0870 chunk 86 optimal weight: 0.3980 chunk 116 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 648 GLN A 983 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10560 Z= 0.181 Angle : 0.576 10.826 14500 Z= 0.272 Chirality : 0.043 0.332 1722 Planarity : 0.005 0.062 1875 Dihedral : 5.968 85.016 1521 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.19 % Allowed : 13.93 % Favored : 83.87 % 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: -0.12 (0.22), residues: 1379 helix: 0.86 (0.25), residues: 478 sheet: 0.12 (0.35), residues: 213 loop : -0.79 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 232 HIS 0.004 0.001 HIS A 983 PHE 0.006 0.001 PHE A 107 TYR 0.013 0.001 TYR A 439 ARG 0.014 0.000 ARG A 764 ********************** 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 136 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8437 (mtm-85) cc_final: 0.7672 (tpt170) REVERT: A 147 SER cc_start: 0.8152 (OUTLIER) cc_final: 0.7743 (p) REVERT: A 212 ARG cc_start: 0.7739 (ttt90) cc_final: 0.7466 (tpm170) REVERT: A 523 ARG cc_start: 0.8447 (ttm-80) cc_final: 0.8217 (ttm110) REVERT: A 767 THR cc_start: 0.8083 (p) cc_final: 0.7668 (t) REVERT: A 768 ASN cc_start: 0.8361 (m110) cc_final: 0.8140 (m110) REVERT: A 844 GLN cc_start: 0.8273 (tt0) cc_final: 0.7992 (tt0) REVERT: A 954 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7783 (pp) REVERT: A 959 SER cc_start: 0.7968 (p) cc_final: 0.7513 (m) REVERT: A 1097 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8572 (mtmm) REVERT: B 44 MET cc_start: 0.7565 (mmp) cc_final: 0.6877 (mtt) outliers start: 23 outliers final: 15 residues processed: 127 average time/residue: 0.9677 time to fit residues: 135.0864 Evaluate side-chains 127 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1097 LYS Chi-restraints excluded: chain A residue 1354 LEU Chi-restraints excluded: chain A residue 1383 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.0980 chunk 100 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 983 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.091532 restraints weight = 32344.340| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.32 r_work: 0.2871 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10560 Z= 0.184 Angle : 0.572 11.120 14500 Z= 0.272 Chirality : 0.043 0.343 1722 Planarity : 0.005 0.077 1875 Dihedral : 5.803 80.028 1521 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.81 % Allowed : 14.60 % Favored : 83.59 % 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: -0.08 (0.22), residues: 1379 helix: 0.89 (0.25), residues: 478 sheet: 0.13 (0.35), residues: 218 loop : -0.75 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 232 HIS 0.003 0.001 HIS A 675 PHE 0.007 0.001 PHE A 107 TYR 0.013 0.001 TYR A 439 ARG 0.008 0.000 ARG A 267 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3417.56 seconds wall clock time: 60 minutes 58.28 seconds (3658.28 seconds total)