Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 11:57:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qq5_4618/08_2023/6qq5_4618_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qq5_4618/08_2023/6qq5_4618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qq5_4618/08_2023/6qq5_4618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qq5_4618/08_2023/6qq5_4618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qq5_4618/08_2023/6qq5_4618_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qq5_4618/08_2023/6qq5_4618_updated.pdb" } resolution = 3.9 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= 0.011 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 Fe 6 7.16 5 S 46 5.16 5 C 7835 2.51 5 N 1970 2.21 5 O 1970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 6": "NH1" <-> "NH2" Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ASP 102": "OD1" <-> "OD2" Residue "A ASP 112": "OD1" <-> "OD2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A ASP 133": "OD1" <-> "OD2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A ASP 268": "OD1" <-> "OD2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 359": "OD1" <-> "OD2" Residue "A ASP 444": "OD1" <-> "OD2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A GLU 559": "OE1" <-> "OE2" Residue "A GLU 569": "OE1" <-> "OE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A ARG 575": "NH1" <-> "NH2" Residue "A TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 724": "OD1" <-> "OD2" Residue "B ARG 6": "NH1" <-> "NH2" Residue "B TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ASP 52": "OD1" <-> "OD2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B ASP 102": "OD1" <-> "OD2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B ASP 162": "OD1" <-> "OD2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B ASP 268": "OD1" <-> "OD2" Residue "B PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 317": "OD1" <-> "OD2" Residue "B ASP 359": "OD1" <-> "OD2" Residue "B TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 444": "OD1" <-> "OD2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B ARG 471": "NH1" <-> "NH2" Residue "B GLU 559": "OE1" <-> "OE2" Residue "B GLU 572": "OE1" <-> "OE2" Residue "B ARG 575": "NH1" <-> "NH2" Residue "B TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "B ASP 711": "OD1" <-> "OD2" Residue "B PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 724": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 11829 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 5825 Classifications: {'peptide': 738} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 702} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 5828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 5828 Classifications: {'peptide': 738} Link IDs: {'PTRANS': 35, 'TRANS': 702} Chain breaks: 1 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.35, per 1000 atoms: 0.54 Number of scatterers: 11829 At special positions: 0 Unit cell: (75.97, 118.77, 108.07, 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) Fe 6 26.01 Ca 2 19.99 S 46 16.00 O 1970 8.00 N 1970 7.00 C 7835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.54 Conformation dependent library (CDL) restraints added in 1.8 seconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2664 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 73 helices and 0 sheets defined 52.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 5 through 31 removed outlier: 4.078A pdb=" N ILE A 12 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LEU A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU A 28 " --> pdb=" O PHE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 removed outlier: 3.844A pdb=" N ILE A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 83 through 100 removed outlier: 4.339A pdb=" N LEU A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.604A pdb=" N ALA A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA A 118 " --> pdb=" O PRO A 114 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG A 120 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 159 removed outlier: 4.216A pdb=" N ALA A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 198 removed outlier: 3.997A pdb=" N HIS A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 253 removed outlier: 3.652A pdb=" N LEU A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 303 removed outlier: 3.815A pdb=" N LEU A 282 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS A 284 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 289 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 292 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 295 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 308 No H-bonds generated for 'chain 'A' and resid 305 through 308' Processing helix chain 'A' and resid 324 through 354 removed outlier: 3.898A pdb=" N ALA A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Proline residue: A 352 - end of helix Processing helix chain 'A' and resid 363 through 389 removed outlier: 3.518A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TRP A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 438 removed outlier: 3.768A pdb=" N GLY A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 446 through 458 removed outlier: 3.851A pdb=" N LEU A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 474 through 477 No H-bonds generated for 'chain 'A' and resid 474 through 477' Processing helix chain 'A' and resid 493 through 507 removed outlier: 4.166A pdb=" N THR A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 520 No H-bonds generated for 'chain 'A' and resid 518 through 520' Processing helix chain 'A' and resid 522 through 525 No H-bonds generated for 'chain 'A' and resid 522 through 525' Processing helix chain 'A' and resid 535 through 538 Processing helix chain 'A' and resid 546 through 554 removed outlier: 3.775A pdb=" N SER A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 559 No H-bonds generated for 'chain 'A' and resid 557 through 559' Processing helix chain 'A' and resid 561 through 564 No H-bonds generated for 'chain 'A' and resid 561 through 564' Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 589 through 602 removed outlier: 4.588A pdb=" N VAL A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA A 597 " --> pdb=" O PHE A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 No H-bonds generated for 'chain 'A' and resid 606 through 609' Processing helix chain 'A' and resid 626 through 635 removed outlier: 3.509A pdb=" N PHE A 635 " --> pdb=" O HIS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 647 No H-bonds generated for 'chain 'A' and resid 644 through 647' Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 671 through 677 Processing helix chain 'A' and resid 679 through 682 No H-bonds generated for 'chain 'A' and resid 679 through 682' Processing helix chain 'A' and resid 684 through 696 Processing helix chain 'A' and resid 700 through 703 No H-bonds generated for 'chain 'A' and resid 700 through 703' Processing helix chain 'A' and resid 721 through 741 removed outlier: 4.629A pdb=" N VAL A 726 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 727 " --> pdb=" O GLY A 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 17 removed outlier: 4.138A pdb=" N ILE B 12 " --> pdb=" O TRP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.753A pdb=" N TYR B 30 " --> pdb=" O GLY B 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 26 through 30' Processing helix chain 'B' and resid 51 through 64 removed outlier: 3.596A pdb=" N LEU B 55 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 86 through 98 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 113 through 116 No H-bonds generated for 'chain 'B' and resid 113 through 116' Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.728A pdb=" N ALA B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 removed outlier: 3.789A pdb=" N GLN B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR B 156 " --> pdb=" O THR B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 198 removed outlier: 3.769A pdb=" N THR B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE B 194 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 253 removed outlier: 3.528A pdb=" N SER B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 234 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 235 " --> pdb=" O MET B 231 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 236 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE B 253 " --> pdb=" O TRP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.619A pdb=" N LEU B 282 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY B 283 " --> pdb=" O ARG B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 279 through 283' Processing helix chain 'B' and resid 285 through 303 removed outlier: 3.993A pdb=" N VAL B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 308 No H-bonds generated for 'chain 'B' and resid 305 through 308' Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.820A pdb=" N THR B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA B 335 " --> pdb=" O HIS B 331 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 354 No H-bonds generated for 'chain 'B' and resid 351 through 354' Processing helix chain 'B' and resid 364 through 384 removed outlier: 3.719A pdb=" N ILE B 369 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TRP B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 373 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 376 " --> pdb=" O TRP B 372 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 No H-bonds generated for 'chain 'B' and resid 386 through 389' Processing helix chain 'B' and resid 413 through 433 removed outlier: 3.539A pdb=" N GLY B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY B 422 " --> pdb=" O GLY B 418 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 438 No H-bonds generated for 'chain 'B' and resid 435 through 438' Processing helix chain 'B' and resid 446 through 458 Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 474 through 477 No H-bonds generated for 'chain 'B' and resid 474 through 477' Processing helix chain 'B' and resid 493 through 507 removed outlier: 3.524A pdb=" N ALA B 497 " --> pdb=" O PHE B 493 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 520 No H-bonds generated for 'chain 'B' and resid 518 through 520' Processing helix chain 'B' and resid 535 through 538 Processing helix chain 'B' and resid 546 through 554 removed outlier: 3.503A pdb=" N ALA B 553 " --> pdb=" O MET B 549 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 554 " --> pdb=" O ALA B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 559 No H-bonds generated for 'chain 'B' and resid 557 through 559' Processing helix chain 'B' and resid 561 through 564 No H-bonds generated for 'chain 'B' and resid 561 through 564' Processing helix chain 'B' and resid 581 through 583 No H-bonds generated for 'chain 'B' and resid 581 through 583' Processing helix chain 'B' and resid 589 through 602 removed outlier: 4.254A pdb=" N VAL B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 595 " --> pdb=" O MET B 591 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA B 597 " --> pdb=" O PHE B 593 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 609 No H-bonds generated for 'chain 'B' and resid 606 through 609' Processing helix chain 'B' and resid 626 through 635 removed outlier: 3.575A pdb=" N LEU B 634 " --> pdb=" O ALA B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 667 No H-bonds generated for 'chain 'B' and resid 664 through 667' Processing helix chain 'B' and resid 672 through 682 removed outlier: 3.871A pdb=" N MET B 678 " --> pdb=" O GLY B 674 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 681 " --> pdb=" O LEU B 677 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 682 " --> pdb=" O MET B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 694 removed outlier: 3.623A pdb=" N PHE B 691 " --> pdb=" O GLY B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 703 No H-bonds generated for 'chain 'B' and resid 700 through 703' Processing helix chain 'B' and resid 721 through 741 removed outlier: 4.606A pdb=" N VAL B 726 " --> pdb=" O PHE B 722 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET B 734 " --> pdb=" O GLY B 730 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1086 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: 3.18 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 4901 1.38 - 1.55: 7199 1.55 - 1.71: 29 1.71 - 1.87: 88 1.87 - 2.04: 16 Bond restraints: 12233 Sorted by residual: bond pdb=" C THR A 276 " pdb=" N PRO A 277 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.62e+00 bond pdb=" C THR B 276 " pdb=" N PRO B 277 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.46e+00 bond pdb=" N ARG A 168 " pdb=" CA ARG A 168 " ideal model delta sigma weight residual 1.462 1.489 -0.027 1.48e-02 4.57e+03 3.31e+00 bond pdb=" CB GLN A 296 " pdb=" CG GLN A 296 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.11e+00 bond pdb=" N ARG B 168 " pdb=" CA ARG B 168 " ideal model delta sigma weight residual 1.462 1.486 -0.024 1.48e-02 4.57e+03 2.66e+00 ... (remaining 12228 not shown) Histogram of bond angle deviations from ideal: 87.84 - 106.04: 331 106.04 - 124.24: 15795 124.24 - 142.44: 614 142.44 - 160.65: 0 160.65 - 178.85: 8 Bond angle restraints: 16748 Sorted by residual: angle pdb=" C ALA A 163 " pdb=" N PRO A 164 " pdb=" CA PRO A 164 " ideal model delta sigma weight residual 118.85 128.43 -9.58 1.09e+00 8.42e-01 7.73e+01 angle pdb=" N VAL A 560 " pdb=" CA VAL A 560 " pdb=" C VAL A 560 " ideal model delta sigma weight residual 113.42 106.65 6.77 1.17e+00 7.31e-01 3.35e+01 angle pdb=" N ILE A 712 " pdb=" CA ILE A 712 " pdb=" C ILE A 712 " ideal model delta sigma weight residual 112.96 107.18 5.78 1.00e+00 1.00e+00 3.34e+01 angle pdb=" N VAL B 560 " pdb=" CA VAL B 560 " pdb=" C VAL B 560 " ideal model delta sigma weight residual 113.42 107.22 6.20 1.17e+00 7.31e-01 2.81e+01 angle pdb=" C GLU A 407 " pdb=" N TYR A 408 " pdb=" CA TYR A 408 " ideal model delta sigma weight residual 121.54 130.56 -9.02 1.91e+00 2.74e-01 2.23e+01 ... (remaining 16743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 6067 17.66 - 35.32: 577 35.32 - 52.98: 117 52.98 - 70.64: 19 70.64 - 88.30: 14 Dihedral angle restraints: 6794 sinusoidal: 2602 harmonic: 4192 Sorted by residual: dihedral pdb=" CA PHE A 461 " pdb=" C PHE A 461 " pdb=" N TYR A 462 " pdb=" CA TYR A 462 " ideal model delta harmonic sigma weight residual 180.00 154.22 25.78 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA SER B 169 " pdb=" C SER B 169 " pdb=" N ARG B 170 " pdb=" CA ARG B 170 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ARG B 168 " pdb=" C ARG B 168 " pdb=" N SER B 169 " pdb=" CA SER B 169 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 6791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1226 0.052 - 0.104: 431 0.104 - 0.155: 91 0.155 - 0.207: 22 0.207 - 0.259: 4 Chirality restraints: 1774 Sorted by residual: chirality pdb=" CA THR B 276 " pdb=" N THR B 276 " pdb=" C THR B 276 " pdb=" CB THR B 276 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA THR A 276 " pdb=" N THR A 276 " pdb=" C THR A 276 " pdb=" CB THR A 276 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA TRP A 215 " pdb=" N TRP A 215 " pdb=" C TRP A 215 " pdb=" CB TRP A 215 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1771 not shown) Planarity restraints: 2077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 546 " 0.049 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PRO A 547 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 547 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 547 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 546 " -0.044 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO B 547 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 547 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 547 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 588 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO B 589 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 589 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 589 " 0.032 5.00e-02 4.00e+02 ... (remaining 2074 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 42 2.41 - 3.04: 6134 3.04 - 3.66: 17597 3.66 - 4.28: 26310 4.28 - 4.90: 44136 Nonbonded interactions: 94219 Sorted by model distance: nonbonded pdb=" CE1 HIS B 486 " pdb="FE FE B 803 " model vdw 1.792 2.480 nonbonded pdb=" CE1 HIS A 486 " pdb="FE FE A 803 " model vdw 1.815 2.480 nonbonded pdb=" ND1 HIS B 486 " pdb="FE FE B 803 " model vdw 1.946 2.340 nonbonded pdb=" ND1 HIS A 486 " pdb="FE FE A 803 " model vdw 1.948 2.340 nonbonded pdb=" NE2 HIS A 538 " pdb="FE FE A 803 " model vdw 2.078 2.340 ... (remaining 94214 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 395 or (resid 396 and (name N or name CA or name \ C or name O or name CB )) or resid 397 through 743 or resid 801 through 804)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.360 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 32.370 Find NCS groups from input model: 0.610 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.007 0.096 12233 Z= 0.460 Angle : 1.071 10.130 16748 Z= 0.567 Chirality : 0.056 0.259 1774 Planarity : 0.007 0.073 2077 Dihedral : 14.963 88.295 4130 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.09 (0.14), residues: 1468 helix: -4.06 (0.09), residues: 924 sheet: None (None), residues: 0 loop : -3.68 (0.21), residues: 544 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.340 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2708 time to fit residues: 89.5799 Evaluate side-chains 197 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 61 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 HIS ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN A 385 ASN A 473 HIS B 89 HIS ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 12233 Z= 0.190 Angle : 0.671 14.288 16748 Z= 0.324 Chirality : 0.040 0.154 1774 Planarity : 0.005 0.052 2077 Dihedral : 7.385 75.274 1636 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.34 (0.18), residues: 1468 helix: -2.64 (0.14), residues: 912 sheet: None (None), residues: 0 loop : -3.08 (0.23), residues: 556 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 208 time to evaluate : 1.249 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 211 average time/residue: 0.2364 time to fit residues: 72.5139 Evaluate side-chains 197 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 187 time to evaluate : 1.293 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1119 time to fit residues: 3.8302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 167 HIS A 385 ASN A 473 HIS B 62 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 ASN ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 12233 Z= 0.289 Angle : 0.690 15.626 16748 Z= 0.326 Chirality : 0.043 0.155 1774 Planarity : 0.004 0.050 2077 Dihedral : 7.232 72.471 1636 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.20), residues: 1468 helix: -2.03 (0.16), residues: 922 sheet: None (None), residues: 0 loop : -2.75 (0.25), residues: 546 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 1.316 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 201 average time/residue: 0.2453 time to fit residues: 72.0543 Evaluate side-chains 187 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 178 time to evaluate : 1.392 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1274 time to fit residues: 3.9289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 133 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 38 optimal weight: 0.0060 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 12233 Z= 0.313 Angle : 0.690 14.831 16748 Z= 0.326 Chirality : 0.043 0.149 1774 Planarity : 0.004 0.050 2077 Dihedral : 7.145 73.384 1636 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.21), residues: 1468 helix: -1.70 (0.16), residues: 918 sheet: None (None), residues: 0 loop : -2.56 (0.25), residues: 550 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 191 time to evaluate : 1.396 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 202 average time/residue: 0.2357 time to fit residues: 68.9666 Evaluate side-chains 194 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 182 time to evaluate : 1.298 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1145 time to fit residues: 4.1672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 35 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 GLN A 473 HIS ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 12233 Z= 0.177 Angle : 0.606 12.650 16748 Z= 0.288 Chirality : 0.039 0.144 1774 Planarity : 0.004 0.047 2077 Dihedral : 6.801 77.687 1636 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.21), residues: 1468 helix: -1.33 (0.17), residues: 908 sheet: None (None), residues: 0 loop : -2.43 (0.26), residues: 560 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 194 time to evaluate : 1.271 Fit side-chains outliers start: 17 outliers final: 4 residues processed: 199 average time/residue: 0.2326 time to fit residues: 67.5204 Evaluate side-chains 184 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 180 time to evaluate : 1.337 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1105 time to fit residues: 2.5413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN A 391 GLN A 473 HIS ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 12233 Z= 0.284 Angle : 0.666 14.598 16748 Z= 0.313 Chirality : 0.043 0.246 1774 Planarity : 0.004 0.046 2077 Dihedral : 6.915 72.642 1636 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.22), residues: 1468 helix: -1.20 (0.17), residues: 906 sheet: None (None), residues: 0 loop : -2.32 (0.26), residues: 562 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 177 time to evaluate : 1.324 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 188 average time/residue: 0.2415 time to fit residues: 65.8825 Evaluate side-chains 182 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 171 time to evaluate : 1.292 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1186 time to fit residues: 4.0769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 103 optimal weight: 0.3980 chunk 79 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 HIS ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 12233 Z= 0.196 Angle : 0.622 12.862 16748 Z= 0.292 Chirality : 0.041 0.209 1774 Planarity : 0.004 0.046 2077 Dihedral : 6.761 74.936 1636 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.22), residues: 1468 helix: -0.92 (0.18), residues: 886 sheet: None (None), residues: 0 loop : -2.27 (0.25), residues: 582 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 177 time to evaluate : 1.379 Fit side-chains outliers start: 9 outliers final: 1 residues processed: 182 average time/residue: 0.2452 time to fit residues: 65.0133 Evaluate side-chains 170 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 1.321 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1142 time to fit residues: 1.9230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 13 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 128 optimal weight: 0.3980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 HIS ** A 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 12233 Z= 0.316 Angle : 0.691 14.375 16748 Z= 0.324 Chirality : 0.044 0.268 1774 Planarity : 0.004 0.046 2077 Dihedral : 6.944 72.569 1636 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.22), residues: 1468 helix: -1.06 (0.17), residues: 914 sheet: None (None), residues: 0 loop : -2.14 (0.27), residues: 554 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 172 time to evaluate : 1.388 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 177 average time/residue: 0.2828 time to fit residues: 73.3749 Evaluate side-chains 173 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 168 time to evaluate : 2.071 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1624 time to fit residues: 4.1935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 0.0070 chunk 102 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 130 optimal weight: 0.0570 chunk 86 optimal weight: 0.5980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 HIS ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 12233 Z= 0.194 Angle : 0.630 12.473 16748 Z= 0.297 Chirality : 0.040 0.212 1774 Planarity : 0.004 0.046 2077 Dihedral : 6.710 75.260 1636 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.22), residues: 1468 helix: -0.78 (0.18), residues: 890 sheet: None (None), residues: 0 loop : -2.13 (0.26), residues: 578 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 183 time to evaluate : 1.216 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 183 average time/residue: 0.2383 time to fit residues: 63.9024 Evaluate side-chains 170 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 1.368 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1196 time to fit residues: 2.0205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 96 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 115 optimal weight: 0.3980 chunk 12 optimal weight: 4.9990 chunk 89 optimal weight: 0.0570 chunk 71 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 HIS ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 12233 Z= 0.182 Angle : 0.628 11.759 16748 Z= 0.297 Chirality : 0.040 0.178 1774 Planarity : 0.004 0.046 2077 Dihedral : 6.611 76.004 1636 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.22), residues: 1468 helix: -0.66 (0.18), residues: 894 sheet: None (None), residues: 0 loop : -2.11 (0.26), residues: 574 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 184 time to evaluate : 1.476 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 185 average time/residue: 0.2558 time to fit residues: 70.0079 Evaluate side-chains 176 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 1.420 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1758 time to fit residues: 2.3113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 7.9990 chunk 35 optimal weight: 0.0030 chunk 106 optimal weight: 1.9990 chunk 17 optimal weight: 0.0170 chunk 32 optimal weight: 0.0670 chunk 116 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 119 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 101 optimal weight: 0.0980 overall best weight: 0.0564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 473 HIS ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.140583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.120761 restraints weight = 15467.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.121351 restraints weight = 31742.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.122253 restraints weight = 27237.443| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 12233 Z= 0.166 Angle : 0.606 8.232 16748 Z= 0.291 Chirality : 0.039 0.166 1774 Planarity : 0.003 0.044 2077 Dihedral : 6.426 77.995 1636 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.22), residues: 1468 helix: -0.45 (0.18), residues: 894 sheet: None (None), residues: 0 loop : -2.07 (0.26), residues: 574 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2212.58 seconds wall clock time: 41 minutes 3.42 seconds (2463.42 seconds total)