Starting phenix.real_space_refine on Fri Feb 16 05:09:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7i_23213/02_2024/7l7i_23213_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7i_23213/02_2024/7l7i_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_23213/02_2024/7l7i_23213.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7i_23213/02_2024/7l7i_23213.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7i_23213/02_2024/7l7i_23213_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7i_23213/02_2024/7l7i_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-dev-5238/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: 7.67, per 1000 atoms: 0.53 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: 5.33 Conformation dependent library (CDL) restraints added in 2.6 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: 3.01 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: 4.55 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: 8800 29.46 - 58.91: 197 58.91 - 88.37: 50 88.37 - 117.83: 0 117.83 - 147.29: 2 Dihedral angle restraints: 9049 sinusoidal: 3864 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 9046 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: 0.010 Normalize map: mean=0, sd=1: 2.970 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: 10.990 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 39.880 Find NCS groups from input model: 0.560 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.640 ------------------------------------------------------------------------------- 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 : 14.115 147.285 5701 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.134 0.025 TRP E 109 HIS 0.015 0.004 HIS A 77 PHE 0.092 0.015 PHE A 329 TYR 0.109 0.019 TYR C 223 ARG 0.013 0.001 ARG B 464 *********************** 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 : 1.612 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: 0.3454 time to fit residues: 86.6401 Evaluate side-chains 94 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 591 ARG 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: 0.9990 chunk 102 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 514 HIS B 531 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.2437 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= 0.192 Angle : 0.569 7.581 19723 Z= 0.314 Chirality : 0.042 0.141 2150 Planarity : 0.004 0.032 2520 Dihedral : 7.872 136.551 1997 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.20 % Allowed : 5.76 % 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: 0.34 (0.20), residues: 641 sheet: 0.39 (0.29), residues: 308 loop : 0.10 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 162 HIS 0.004 0.001 HIS C 401 PHE 0.026 0.002 PHE E 103 TYR 0.017 0.002 TYR A 381 ARG 0.005 0.000 ARG A 464 *********************** 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: 19 poor density : 106 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.3027 (ppp) cc_final: 0.1930 (mmt) outliers start: 19 outliers final: 7 residues processed: 121 average time/residue: 0.3005 time to fit residues: 52.7522 Evaluate side-chains 92 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 694 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 159 optimal weight: 0.0470 chunk 171 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 54 optimal weight: 0.1980 chunk 127 optimal weight: 3.9990 overall best weight: 2.0484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 401 HIS ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 306 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14677 Z= 0.311 Angle : 0.572 7.594 19723 Z= 0.310 Chirality : 0.043 0.146 2150 Planarity : 0.004 0.038 2520 Dihedral : 7.334 129.232 1990 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.58 % Allowed : 6.90 % Favored : 91.52 % 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: 0.16 (0.20), residues: 1763 helix: 0.47 (0.20), residues: 645 sheet: 0.09 (0.28), residues: 327 loop : -0.03 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 297 HIS 0.005 0.001 HIS B 490 PHE 0.027 0.002 PHE A 329 TYR 0.021 0.002 TYR A 434 ARG 0.006 0.000 ARG A 464 *********************** 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 107 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.3017 (ppp) cc_final: 0.2077 (mmt) outliers start: 25 outliers final: 15 residues processed: 102 average time/residue: 0.3175 time to fit residues: 47.5879 Evaluate side-chains 91 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 694 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 169 optimal weight: 20.0000 chunk 83 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 HIS B 189 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14677 Z= 0.171 Angle : 0.491 7.438 19723 Z= 0.266 Chirality : 0.040 0.140 2150 Planarity : 0.003 0.031 2520 Dihedral : 7.009 127.602 1990 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.39 % Allowed : 7.91 % 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: 0.38 (0.20), residues: 1763 helix: 0.84 (0.20), residues: 650 sheet: 0.10 (0.28), residues: 335 loop : -0.04 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 297 HIS 0.003 0.001 HIS A 323 PHE 0.013 0.001 PHE A 329 TYR 0.017 0.001 TYR E 9 ARG 0.005 0.000 ARG E 12 *********************** 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 104 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.3021 (ppp) cc_final: 0.2479 (mmt) outliers start: 22 outliers final: 14 residues processed: 97 average time/residue: 0.3075 time to fit residues: 43.9947 Evaluate side-chains 89 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 694 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 0.1980 chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 40.0000 chunk 125 optimal weight: 0.4980 chunk 69 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 HIS A 633 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14677 Z= 0.165 Angle : 0.480 8.399 19723 Z= 0.257 Chirality : 0.040 0.134 2150 Planarity : 0.003 0.032 2520 Dihedral : 6.812 127.199 1990 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.27 % Allowed : 8.23 % Favored : 90.51 % 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: 0.98 (0.21), residues: 652 sheet: 0.10 (0.28), residues: 347 loop : -0.03 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 297 HIS 0.012 0.001 HIS A 633 PHE 0.010 0.001 PHE A 329 TYR 0.016 0.001 TYR A 434 ARG 0.006 0.000 ARG B 620 *********************** 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 106 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 591 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.6503 (ptm160) REVERT: E 1 MET cc_start: 0.3045 (ppp) cc_final: 0.2706 (mmt) outliers start: 20 outliers final: 13 residues processed: 99 average time/residue: 0.2616 time to fit residues: 40.1758 Evaluate side-chains 91 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 694 LEU 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: 0.6980 chunk 33 optimal weight: 30.0000 chunk 99 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 169 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 88 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 HIS ** 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: 0.6740 moved from start: 0.3690 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= 0.160 Angle : 0.463 9.217 19723 Z= 0.248 Chirality : 0.040 0.140 2150 Planarity : 0.003 0.033 2520 Dihedral : 6.704 127.861 1990 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.33 % Allowed : 8.61 % Favored : 90.06 % 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: 0.54 (0.20), residues: 1763 helix: 1.08 (0.21), residues: 655 sheet: 0.15 (0.28), residues: 342 loop : -0.04 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 297 HIS 0.003 0.001 HIS A 323 PHE 0.009 0.001 PHE A 329 TYR 0.016 0.001 TYR E 9 ARG 0.004 0.000 ARG B 620 *********************** 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 103 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 591 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.6664 (ptm160) outliers start: 21 outliers final: 16 residues processed: 98 average time/residue: 0.2682 time to fit residues: 40.3115 Evaluate side-chains 93 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 694 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 40.0000 chunk 96 optimal weight: 0.2980 chunk 123 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 168 optimal weight: 30.0000 chunk 105 optimal weight: 2.9990 chunk 102 optimal weight: 0.0770 chunk 77 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.0744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 365 ASN A 189 HIS A 633 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14677 Z= 0.187 Angle : 0.482 9.583 19723 Z= 0.255 Chirality : 0.040 0.137 2150 Planarity : 0.003 0.034 2520 Dihedral : 6.679 128.739 1988 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.33 % Allowed : 9.05 % 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: 0.56 (0.20), residues: 1763 helix: 1.12 (0.21), residues: 654 sheet: 0.11 (0.28), residues: 339 loop : -0.03 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 297 HIS 0.014 0.001 HIS A 633 PHE 0.011 0.001 PHE A 329 TYR 0.025 0.001 TYR E 9 ARG 0.003 0.000 ARG B 620 *********************** 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 100 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 591 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7641 (ptp-170) outliers start: 21 outliers final: 14 residues processed: 95 average time/residue: 0.2794 time to fit residues: 40.7688 Evaluate side-chains 93 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 694 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.5980 chunk 100 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 chunk 15 optimal weight: 50.0000 chunk 132 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.6738 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14677 Z= 0.157 Angle : 0.466 10.534 19723 Z= 0.247 Chirality : 0.039 0.140 2150 Planarity : 0.003 0.071 2520 Dihedral : 6.483 128.999 1984 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.14 % Allowed : 9.49 % Favored : 89.37 % 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: 0.58 (0.20), residues: 1763 helix: 1.14 (0.21), residues: 663 sheet: 0.18 (0.28), residues: 327 loop : -0.05 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 297 HIS 0.004 0.001 HIS A 323 PHE 0.009 0.001 PHE A 329 TYR 0.015 0.001 TYR A 434 ARG 0.006 0.000 ARG A 456 *********************** 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 100 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 95 average time/residue: 0.2603 time to fit residues: 38.9187 Evaluate side-chains 94 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 694 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 0.7980 chunk 147 optimal weight: 0.4980 chunk 157 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 148 optimal weight: 0.4980 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 HIS ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6722 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14677 Z= 0.141 Angle : 0.458 11.023 19723 Z= 0.244 Chirality : 0.039 0.138 2150 Planarity : 0.003 0.061 2520 Dihedral : 6.436 128.417 1984 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.01 % Allowed : 9.75 % Favored : 89.24 % 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: 0.65 (0.20), residues: 1763 helix: 1.22 (0.21), residues: 660 sheet: 0.25 (0.28), residues: 327 loop : -0.05 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 297 HIS 0.009 0.001 HIS A 633 PHE 0.009 0.001 PHE B 337 TYR 0.015 0.001 TYR A 434 ARG 0.003 0.000 ARG B 620 *********************** 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 99 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 259 MET cc_start: 0.2100 (pmm) cc_final: 0.1790 (ptp) outliers start: 16 outliers final: 13 residues processed: 96 average time/residue: 0.2469 time to fit residues: 37.7561 Evaluate side-chains 93 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 683 THR 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: 3.9990 chunk 78 optimal weight: 0.0770 chunk 115 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 overall best weight: 0.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 HIS ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.4066 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= 0.146 Angle : 0.461 10.518 19723 Z= 0.245 Chirality : 0.039 0.139 2150 Planarity : 0.003 0.055 2520 Dihedral : 6.394 129.034 1984 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.89 % Allowed : 10.13 % Favored : 88.99 % 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: 1.24 (0.21), residues: 659 sheet: 0.32 (0.28), residues: 337 loop : -0.07 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 297 HIS 0.005 0.001 HIS A 633 PHE 0.008 0.001 PHE B 337 TYR 0.015 0.001 TYR A 434 ARG 0.002 0.000 ARG C 150 ********************** 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 95 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 14 residues processed: 92 average time/residue: 0.2596 time to fit residues: 38.0292 Evaluate side-chains 94 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 683 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 20 optimal weight: 40.0000 chunk 38 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 HIS ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.123752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.078582 restraints weight = 32333.118| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.76 r_work: 0.3160 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14677 Z= 0.218 Angle : 0.504 10.037 19723 Z= 0.266 Chirality : 0.040 0.180 2150 Planarity : 0.003 0.051 2520 Dihedral : 6.503 131.166 1984 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.89 % Allowed : 10.13 % Favored : 88.99 % 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: 0.58 (0.20), residues: 1763 helix: 1.16 (0.21), residues: 659 sheet: 0.22 (0.28), residues: 341 loop : -0.10 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 297 HIS 0.004 0.001 HIS A 633 PHE 0.014 0.001 PHE A 329 TYR 0.018 0.001 TYR A 434 ARG 0.003 0.000 ARG A 464 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2777.43 seconds wall clock time: 51 minutes 57.43 seconds (3117.43 seconds total)