Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 7 07:30:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7i_23213/10_2023/7l7i_23213_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7i_23213/10_2023/7l7i_23213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7i_23213/10_2023/7l7i_23213.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7i_23213/10_2023/7l7i_23213.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7i_23213/10_2023/7l7i_23213_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7i_23213/10_2023/7l7i_23213_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 72 5.16 5 C 9125 2.51 5 N 2447 2.21 5 O 2775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 157": "OE1" <-> "OE2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 366": "OE1" <-> "OE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 580": "OE1" <-> "OE2" Residue "B TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 14425 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3229 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 396} Chain: "A" Number of atoms: 5107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5107 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 15, 'TRANS': 612} Chain breaks: 1 Chain: "B" Number of atoms: 5107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5107 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 15, 'TRANS': 612} Chain breaks: 1 Chain: "E" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 920 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.36, per 1000 atoms: 0.51 Number of scatterers: 14425 At special positions: 0 Unit cell: (102.564, 105.82, 142.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 6 15.00 O 2775 8.00 N 2447 7.00 C 9125 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.34 Conformation dependent library (CDL) restraints added in 1.9 seconds 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3348 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 12 sheets defined 39.2% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'C' and resid 14 through 19 removed outlier: 4.159A pdb=" N ALA C 19 " --> pdb=" O THR C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 88 through 95 Processing helix chain 'C' and resid 109 through 112 No H-bonds generated for 'chain 'C' and resid 109 through 112' Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'C' and resid 193 through 196 Processing helix chain 'C' and resid 200 through 208 removed outlier: 4.636A pdb=" N GLU C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS C 208 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 231 through 233 No H-bonds generated for 'chain 'C' and resid 231 through 233' Processing helix chain 'C' and resid 261 through 280 removed outlier: 3.908A pdb=" N GLU C 273 " --> pdb=" O ALA C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 299 Processing helix chain 'C' and resid 306 through 329 removed outlier: 3.551A pdb=" N MET C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 346 removed outlier: 3.751A pdb=" N LYS C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 363 Processing helix chain 'C' and resid 367 through 380 removed outlier: 3.565A pdb=" N GLY C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LYS C 376 " --> pdb=" O GLY C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 409 Processing helix chain 'C' and resid 412 through 419 Processing helix chain 'A' and resid 26 through 35 removed outlier: 3.768A pdb=" N SER A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 65 removed outlier: 3.529A pdb=" N GLU A 47 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 48 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN A 51 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP A 54 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 56 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR A 65 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 70 Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 406 through 427 removed outlier: 3.570A pdb=" N ASN A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 451 removed outlier: 4.574A pdb=" N GLN A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASN A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 462 removed outlier: 4.754A pdb=" N GLU A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 524 through 532 removed outlier: 4.505A pdb=" N VAL A 530 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 567 Processing helix chain 'A' and resid 569 through 578 Processing helix chain 'A' and resid 608 through 616 removed outlier: 3.523A pdb=" N ALA A 616 " --> pdb=" O ARG A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 628 removed outlier: 3.820A pdb=" N TYR A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N MET A 628 " --> pdb=" O THR A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 652 Processing helix chain 'A' and resid 657 through 673 removed outlier: 3.816A pdb=" N ILE A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 696 removed outlier: 3.794A pdb=" N ARG A 687 " --> pdb=" O THR A 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 removed outlier: 3.554A pdb=" N SER B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 65 removed outlier: 3.662A pdb=" N LEU B 48 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 49 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN B 51 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 56 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS B 58 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER B 63 " --> pdb=" O ARG B 60 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR B 65 " --> pdb=" O GLU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 70 Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.810A pdb=" N ALA B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 143 Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 200 through 211 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 306 through 317 Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 406 through 429 removed outlier: 3.552A pdb=" N LYS B 410 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS B 414 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 417 " --> pdb=" O LYS B 414 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE B 424 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 428 " --> pdb=" O THR B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 451 removed outlier: 3.782A pdb=" N LYS B 436 " --> pdb=" O GLU B 432 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLN B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ASN B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 462 removed outlier: 3.764A pdb=" N GLU B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 483 Processing helix chain 'B' and resid 499 through 503 Processing helix chain 'B' and resid 506 through 514 removed outlier: 4.717A pdb=" N ARG B 510 " --> pdb=" O PHE B 507 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 512 " --> pdb=" O GLU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 532 removed outlier: 4.136A pdb=" N TYR B 528 " --> pdb=" O PRO B 524 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 578 removed outlier: 5.054A pdb=" N ASN B 570 " --> pdb=" O THR B 566 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 616 removed outlier: 3.630A pdb=" N ALA B 616 " --> pdb=" O ARG B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 628 removed outlier: 3.504A pdb=" N GLY B 626 " --> pdb=" O ASN B 622 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR B 627 " --> pdb=" O SER B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 652 Processing helix chain 'B' and resid 657 through 674 Processing helix chain 'B' and resid 681 through 696 removed outlier: 4.003A pdb=" N ARG B 687 " --> pdb=" O THR B 683 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG B 690 " --> pdb=" O ASN B 686 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 77 through 80 removed outlier: 6.439A pdb=" N HIS C 56 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU C 134 " --> pdb=" O HIS C 56 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LYS C 58 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE C 132 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS C 60 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N PHE C 130 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N HIS C 104 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL C 37 " --> pdb=" O HIS C 104 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU C 106 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS C 35 " --> pdb=" O LEU C 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 148 through 154 removed outlier: 6.376A pdb=" N GLN C 214 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU C 169 " --> pdb=" O LYS C 248 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N PHE C 250 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR C 167 " --> pdb=" O PHE C 250 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP C 182 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N CYS C 176 " --> pdb=" O MET C 180 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N MET C 180 " --> pdb=" O CYS C 176 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 171 through 174 removed outlier: 6.931A pdb=" N HIS A 189 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL A 148 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE A 187 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL A 150 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LYS A 185 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR A 152 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY A 183 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU A 80 " --> pdb=" O PRO A 217 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR A 219 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE A 221 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.787A pdb=" N ALA A 325 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL A 365 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N PHE A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 540 through 543 removed outlier: 6.240A pdb=" N ILE A 519 " --> pdb=" O ILE A 494 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 585 through 588 removed outlier: 4.117A pdb=" N LYS A 585 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 285 through 287 removed outlier: 3.681A pdb=" N GLU B 223 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLN B 287 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N PHE B 221 " --> pdb=" O GLN B 287 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 78 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N PHE B 221 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU B 80 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N GLU B 223 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 147 " --> pdb=" O HIS B 189 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 368 through 371 removed outlier: 6.913A pdb=" N LEU B 363 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY B 387 " --> pdb=" O LYS B 362 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TYR B 364 " --> pdb=" O GLY B 387 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 389 " --> pdb=" O TYR B 364 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 325 " --> pdb=" O VAL B 343 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 540 through 543 Processing sheet with id= J, first strand: chain 'B' and resid 585 through 588 removed outlier: 4.027A pdb=" N LYS B 585 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 99 through 101 removed outlier: 6.556A pdb=" N ALA E 6 " --> pdb=" O SER E 100 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 28 through 32 569 hydrogen bonds defined for protein. 1440 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.31 Time building geometry restraints manager: 5.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2489 1.28 - 1.41: 3548 1.41 - 1.55: 8492 1.55 - 1.69: 31 1.69 - 1.82: 117 Bond restraints: 14677 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.527 0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.537 0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" C ARG B 182 " pdb=" O ARG B 182 " ideal model delta sigma weight residual 1.235 1.141 0.094 1.25e-02 6.40e+03 5.65e+01 bond pdb=" N ARG C 175 " pdb=" CA ARG C 175 " ideal model delta sigma weight residual 1.457 1.368 0.088 1.24e-02 6.50e+03 5.09e+01 bond pdb=" C ARG B 591 " pdb=" O ARG B 591 " ideal model delta sigma weight residual 1.236 1.166 0.071 1.28e-02 6.10e+03 3.06e+01 ... (remaining 14672 not shown) Histogram of bond angle deviations from ideal: 97.53 - 105.12: 189 105.12 - 112.71: 6814 112.71 - 120.30: 7225 120.30 - 127.88: 5422 127.88 - 135.47: 73 Bond angle restraints: 19723 Sorted by residual: angle pdb=" CA ARG B 182 " pdb=" C ARG B 182 " pdb=" N GLY B 183 " ideal model delta sigma weight residual 116.38 126.19 -9.81 1.35e+00 5.49e-01 5.28e+01 angle pdb=" CA PHE A 329 " pdb=" CB PHE A 329 " pdb=" CG PHE A 329 " ideal model delta sigma weight residual 113.80 120.16 -6.36 1.00e+00 1.00e+00 4.05e+01 angle pdb=" CA ASP C 195 " pdb=" CB ASP C 195 " pdb=" CG ASP C 195 " ideal model delta sigma weight residual 112.60 118.77 -6.17 1.00e+00 1.00e+00 3.81e+01 angle pdb=" N ARG C 184 " pdb=" CA ARG C 184 " pdb=" C ARG C 184 " ideal model delta sigma weight residual 108.60 117.55 -8.95 1.46e+00 4.69e-01 3.76e+01 angle pdb=" CA PHE A 221 " pdb=" CB PHE A 221 " pdb=" CG PHE A 221 " ideal model delta sigma weight residual 113.80 119.35 -5.55 1.00e+00 1.00e+00 3.08e+01 ... (remaining 19718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.46: 8747 29.46 - 58.91: 196 58.91 - 88.37: 48 88.37 - 117.83: 0 117.83 - 147.29: 2 Dihedral angle restraints: 8993 sinusoidal: 3808 harmonic: 5185 Sorted by residual: dihedral pdb=" CA GLU C 192 " pdb=" C GLU C 192 " pdb=" N GLY C 193 " pdb=" CA GLY C 193 " ideal model delta harmonic sigma weight residual -180.00 -150.70 -29.30 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA GLN A 287 " pdb=" C GLN A 287 " pdb=" N GLU A 288 " pdb=" CA GLU A 288 " ideal model delta harmonic sigma weight residual -180.00 -151.17 -28.83 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLU A 392 " pdb=" C GLU A 392 " pdb=" N ASP A 393 " pdb=" CA ASP A 393 " ideal model delta harmonic sigma weight residual -180.00 -151.63 -28.37 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 8990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1327 0.078 - 0.155: 658 0.155 - 0.233: 127 0.233 - 0.311: 27 0.311 - 0.388: 11 Chirality restraints: 2150 Sorted by residual: chirality pdb=" CA ARG B 367 " pdb=" N ARG B 367 " pdb=" C ARG B 367 " pdb=" CB ARG B 367 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA ARG B 591 " pdb=" N ARG B 591 " pdb=" C ARG B 591 " pdb=" CB ARG B 591 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA ARG A 367 " pdb=" N ARG A 367 " pdb=" C ARG A 367 " pdb=" CB ARG A 367 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 2147 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 109 " -0.134 2.00e-02 2.50e+03 6.96e-02 1.21e+02 pdb=" CG TRP E 109 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP E 109 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP E 109 " 0.070 2.00e-02 2.50e+03 pdb=" NE1 TRP E 109 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TRP E 109 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP E 109 " 0.105 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 109 " -0.069 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 109 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP E 109 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 297 " -0.078 2.00e-02 2.50e+03 6.04e-02 9.13e+01 pdb=" CG TRP A 297 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 297 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 297 " 0.042 2.00e-02 2.50e+03 pdb=" NE1 TRP A 297 " 0.088 2.00e-02 2.50e+03 pdb=" CE2 TRP A 297 " 0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP A 297 " 0.080 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 297 " -0.075 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 297 " 0.038 2.00e-02 2.50e+03 pdb=" CH2 TRP A 297 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 401 " 0.093 2.00e-02 2.50e+03 6.94e-02 7.22e+01 pdb=" CG HIS C 401 " -0.100 2.00e-02 2.50e+03 pdb=" ND1 HIS C 401 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 HIS C 401 " -0.051 2.00e-02 2.50e+03 pdb=" CE1 HIS C 401 " 0.050 2.00e-02 2.50e+03 pdb=" NE2 HIS C 401 " 0.054 2.00e-02 2.50e+03 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2896 2.82 - 3.34: 14279 3.34 - 3.86: 24011 3.86 - 4.38: 29949 4.38 - 4.90: 49475 Nonbonded interactions: 120610 Sorted by model distance: nonbonded pdb=" CD ARG B 510 " pdb=" O ASN B 590 " model vdw 2.300 3.440 nonbonded pdb=" ND2 ASN B 51 " pdb=" O1A ANP B 801 " model vdw 2.339 2.520 nonbonded pdb=" ND2 ASN A 51 " pdb=" O1A ANP A 801 " model vdw 2.381 2.520 nonbonded pdb=" O1B ANP A 801 " pdb=" O3' ANP A 801 " model vdw 2.479 2.440 nonbonded pdb=" O1B ANP B 801 " pdb=" O3' ANP B 801 " model vdw 2.532 2.440 ... (remaining 120605 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 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: 11.020 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 36.800 Find NCS groups from input model: 0.600 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 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 : 0.013 0.173 14677 Z= 0.822 Angle : 1.762 15.733 19723 Z= 1.160 Chirality : 0.092 0.388 2150 Planarity : 0.013 0.130 2520 Dihedral : 14.057 147.285 5645 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.74 % Favored : 96.09 % Rotamer: Outliers : 0.76 % Allowed : 2.85 % Favored : 96.39 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 2.22 % 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: -1.40 (0.18), residues: 1763 helix: -1.69 (0.16), residues: 660 sheet: 0.19 (0.32), residues: 265 loop : -0.48 (0.21), residues: 838 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 173 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 184 average time/residue: 0.3542 time to fit residues: 89.6334 Evaluate side-chains 94 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 1.773 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2785 time to fit residues: 4.7140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 ASN ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 HIS B 35 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14677 Z= 0.193 Angle : 0.572 7.651 19723 Z= 0.316 Chirality : 0.042 0.140 2150 Planarity : 0.004 0.032 2520 Dihedral : 7.072 137.044 1928 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.08 % Allowed : 5.89 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.24 (0.20), residues: 1763 helix: 0.33 (0.20), residues: 641 sheet: 0.42 (0.29), residues: 306 loop : 0.09 (0.23), residues: 816 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 121 average time/residue: 0.3017 time to fit residues: 53.7206 Evaluate side-chains 91 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 1.721 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1318 time to fit residues: 3.4906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 171 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 54 optimal weight: 0.0970 chunk 127 optimal weight: 0.3980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 189 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14677 Z= 0.215 Angle : 0.519 7.320 19723 Z= 0.284 Chirality : 0.041 0.139 2150 Planarity : 0.003 0.035 2520 Dihedral : 6.529 130.562 1928 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.95 % Allowed : 7.09 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.37 (0.20), residues: 1763 helix: 0.63 (0.20), residues: 646 sheet: 0.15 (0.28), residues: 336 loop : 0.14 (0.23), residues: 781 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 1.771 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 99 average time/residue: 0.3128 time to fit residues: 46.2820 Evaluate side-chains 83 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 1.678 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2923 time to fit residues: 4.8044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 159 optimal weight: 0.2980 chunk 169 optimal weight: 20.0000 chunk 83 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14677 Z= 0.180 Angle : 0.484 7.209 19723 Z= 0.262 Chirality : 0.040 0.138 2150 Planarity : 0.003 0.031 2520 Dihedral : 6.385 130.342 1928 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.76 % Allowed : 7.97 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.47 (0.20), residues: 1763 helix: 0.89 (0.20), residues: 654 sheet: 0.15 (0.28), residues: 345 loop : 0.05 (0.23), residues: 764 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 1.736 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 88 average time/residue: 0.2656 time to fit residues: 36.6441 Evaluate side-chains 76 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 1.718 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1299 time to fit residues: 3.3902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 2 optimal weight: 40.0000 chunk 125 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 HIS A 189 HIS A 531 GLN A 633 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14677 Z= 0.240 Angle : 0.514 8.364 19723 Z= 0.274 Chirality : 0.041 0.146 2150 Planarity : 0.003 0.033 2520 Dihedral : 6.401 131.015 1928 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.82 % Allowed : 8.48 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.20), residues: 1763 helix: 0.95 (0.20), residues: 650 sheet: 0.03 (0.28), residues: 343 loop : -0.05 (0.23), residues: 770 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 1.700 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 89 average time/residue: 0.2790 time to fit residues: 38.5605 Evaluate side-chains 82 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 1.844 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2178 time to fit residues: 4.2974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 169 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 78 optimal weight: 0.0170 chunk 14 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 overall best weight: 1.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 365 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14677 Z= 0.197 Angle : 0.482 8.994 19723 Z= 0.257 Chirality : 0.040 0.142 2150 Planarity : 0.003 0.038 2520 Dihedral : 6.350 132.803 1928 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.76 % Allowed : 8.61 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.48 (0.20), residues: 1763 helix: 1.03 (0.21), residues: 652 sheet: 0.11 (0.28), residues: 339 loop : -0.07 (0.23), residues: 772 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 91 average time/residue: 0.2882 time to fit residues: 41.8590 Evaluate side-chains 82 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 1.792 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2434 time to fit residues: 4.3351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 20.0000 chunk 96 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 142 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14677 Z= 0.242 Angle : 0.508 9.459 19723 Z= 0.269 Chirality : 0.041 0.142 2150 Planarity : 0.003 0.035 2520 Dihedral : 6.356 133.504 1928 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.38 % Allowed : 9.68 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.42 (0.20), residues: 1763 helix: 1.00 (0.21), residues: 652 sheet: -0.00 (0.28), residues: 333 loop : -0.07 (0.23), residues: 778 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 1.570 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 84 average time/residue: 0.2538 time to fit residues: 34.1018 Evaluate side-chains 82 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 1.700 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1320 time to fit residues: 3.4037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 50.0000 chunk 132 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14677 Z= 0.166 Angle : 0.472 10.526 19723 Z= 0.250 Chirality : 0.040 0.137 2150 Planarity : 0.003 0.033 2520 Dihedral : 6.265 134.420 1928 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.13 % Allowed : 9.87 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.53 (0.20), residues: 1763 helix: 1.12 (0.21), residues: 659 sheet: 0.12 (0.28), residues: 325 loop : -0.09 (0.23), residues: 779 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 1.697 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 83 average time/residue: 0.2737 time to fit residues: 36.2424 Evaluate side-chains 79 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.801 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 0.9980 chunk 147 optimal weight: 0.0070 chunk 157 optimal weight: 9.9990 chunk 94 optimal weight: 0.0970 chunk 68 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 148 optimal weight: 0.2980 chunk 156 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14677 Z= 0.122 Angle : 0.452 9.355 19723 Z= 0.241 Chirality : 0.039 0.133 2150 Planarity : 0.003 0.034 2520 Dihedral : 6.076 129.851 1928 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.13 % Allowed : 10.25 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.68 (0.20), residues: 1763 helix: 1.29 (0.21), residues: 657 sheet: 0.21 (0.28), residues: 334 loop : -0.05 (0.23), residues: 772 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 1.684 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 89 average time/residue: 0.2812 time to fit residues: 38.6629 Evaluate side-chains 82 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.596 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 chunk 78 optimal weight: 0.0000 chunk 115 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 0.3980 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14677 Z= 0.164 Angle : 0.477 11.106 19723 Z= 0.252 Chirality : 0.040 0.136 2150 Planarity : 0.003 0.039 2520 Dihedral : 6.116 132.200 1928 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.13 % Allowed : 10.25 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.68 (0.20), residues: 1763 helix: 1.29 (0.21), residues: 657 sheet: 0.28 (0.29), residues: 330 loop : -0.10 (0.23), residues: 776 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 1.631 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 82 average time/residue: 0.2622 time to fit residues: 34.0103 Evaluate side-chains 78 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.750 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.0770 chunk 42 optimal weight: 0.1980 chunk 128 optimal weight: 2.9990 chunk 20 optimal weight: 40.0000 chunk 38 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 122 optimal weight: 0.0770 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.125344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.081259 restraints weight = 32141.198| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 4.30 r_work: 0.3201 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14677 Z= 0.145 Angle : 0.470 10.370 19723 Z= 0.248 Chirality : 0.039 0.164 2150 Planarity : 0.003 0.034 2520 Dihedral : 6.097 131.897 1928 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.13 % Allowed : 10.13 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.70 (0.20), residues: 1763 helix: 1.32 (0.21), residues: 657 sheet: 0.34 (0.28), residues: 339 loop : -0.11 (0.23), residues: 767 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2658.93 seconds wall clock time: 49 minutes 40.49 seconds (2980.49 seconds total)