Starting phenix.real_space_refine on Wed Apr 10 07:59:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjh_14748/04_2024/7zjh_14748.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjh_14748/04_2024/7zjh_14748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjh_14748/04_2024/7zjh_14748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjh_14748/04_2024/7zjh_14748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjh_14748/04_2024/7zjh_14748.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjh_14748/04_2024/7zjh_14748.pdb" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.054 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12476 2.51 5 N 3160 2.21 5 O 3236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 18984 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4746 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 18, 'TRANS': 567} Chain breaks: 4 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 4746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4746 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 18, 'TRANS': 567} Chain breaks: 4 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 4746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4746 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 18, 'TRANS': 567} Chain breaks: 4 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 4746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4746 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 18, 'TRANS': 567} Chain breaks: 4 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 9.77, per 1000 atoms: 0.51 Number of scatterers: 18984 At special positions: 0 Unit cell: (120.189, 151.506, 162.509, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3236 8.00 N 3160 7.00 C 12476 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: 6.54 Conformation dependent library (CDL) restraints added in 3.6 seconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4432 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 6 sheets defined 59.3% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 77 through 86 removed outlier: 3.775A pdb=" N PHE A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 129 through 135 Processing helix chain 'A' and resid 135 through 141 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.674A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.922A pdb=" N LEU A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.953A pdb=" N LEU A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.781A pdb=" N GLU A 289 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 290' Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 366 through 371 removed outlier: 4.367A pdb=" N HIS A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 387 removed outlier: 4.096A pdb=" N LYS A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 413 removed outlier: 3.621A pdb=" N PHE A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 459 Processing helix chain 'A' and resid 470 through 490 removed outlier: 4.213A pdb=" N LEU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 490 " --> pdb=" O SER A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 493 No H-bonds generated for 'chain 'A' and resid 491 through 493' Processing helix chain 'A' and resid 496 through 511 Processing helix chain 'A' and resid 512 through 516 Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.737A pdb=" N MET A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 559 removed outlier: 4.066A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 606 removed outlier: 3.846A pdb=" N GLU A 599 " --> pdb=" O ASP A 595 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N THR A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 650 removed outlier: 3.591A pdb=" N LEU A 637 " --> pdb=" O THR A 633 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASN A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 673 removed outlier: 3.998A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 85 removed outlier: 3.826A pdb=" N SER D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL D 83 " --> pdb=" O ARG D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 93 Processing helix chain 'D' and resid 94 through 104 removed outlier: 3.973A pdb=" N ARG D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP D 101 " --> pdb=" O GLU D 97 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN D 102 " --> pdb=" O TYR D 98 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS D 104 " --> pdb=" O ARG D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 129 through 134 removed outlier: 3.707A pdb=" N VAL D 132 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN D 133 " --> pdb=" O ASP D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 145 removed outlier: 4.242A pdb=" N LEU D 139 " --> pdb=" O CYS D 135 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN D 141 " --> pdb=" O MET D 137 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP D 145 " --> pdb=" O GLN D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 177 through 187 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 232 removed outlier: 3.504A pdb=" N LEU D 230 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN D 232 " --> pdb=" O TYR D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 removed outlier: 4.126A pdb=" N ALA D 265 " --> pdb=" O PRO D 261 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 279 " --> pdb=" O LEU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.811A pdb=" N ILE D 290 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 375 through 389 removed outlier: 3.780A pdb=" N LYS D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU D 381 " --> pdb=" O PRO D 377 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 413 removed outlier: 3.655A pdb=" N PHE D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR D 403 " --> pdb=" O CYS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 removed outlier: 3.813A pdb=" N LEU D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 436 " --> pdb=" O SER D 432 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG D 458 " --> pdb=" O TRP D 454 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG D 459 " --> pdb=" O TYR D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 488 Processing helix chain 'D' and resid 488 through 493 removed outlier: 4.063A pdb=" N MET D 492 " --> pdb=" O VAL D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 4.402A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP D 509 " --> pdb=" O LEU D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 516 Processing helix chain 'D' and resid 525 through 529 removed outlier: 3.554A pdb=" N ILE D 529 " --> pdb=" O SER D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 559 removed outlier: 3.664A pdb=" N PHE D 551 " --> pdb=" O PHE D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 606 removed outlier: 3.851A pdb=" N THR D 604 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 647 removed outlier: 4.268A pdb=" N LEU D 624 " --> pdb=" O GLY D 620 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU D 625 " --> pdb=" O VAL D 621 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 626 " --> pdb=" O VAL D 622 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 627 " --> pdb=" O LEU D 623 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA D 628 " --> pdb=" O LEU D 624 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR D 629 " --> pdb=" O LEU D 625 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D 630 " --> pdb=" O LEU D 626 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU D 631 " --> pdb=" O LEU D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 674 removed outlier: 4.333A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY D 674 " --> pdb=" O GLU D 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 85 Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 151 through 155 removed outlier: 3.567A pdb=" N ASN C 154 " --> pdb=" O PRO C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 176 through 187 Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.760A pdb=" N LEU C 230 " --> pdb=" O VAL C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 257 Processing helix chain 'C' and resid 260 through 282 removed outlier: 4.007A pdb=" N ALA C 265 " --> pdb=" O PRO C 261 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 removed outlier: 3.626A pdb=" N GLU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.511A pdb=" N MET C 372 " --> pdb=" O ARG C 369 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 373 " --> pdb=" O HIS C 370 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 374 " --> pdb=" O ARG C 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 369 through 374' Processing helix chain 'C' and resid 375 through 388 removed outlier: 4.258A pdb=" N LYS C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU C 381 " --> pdb=" O PRO C 377 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 413 Processing helix chain 'C' and resid 432 through 459 removed outlier: 3.649A pdb=" N HIS C 438 " --> pdb=" O LEU C 434 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE C 439 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG C 459 " --> pdb=" O TYR C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 492 removed outlier: 3.591A pdb=" N PHE C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR C 483 " --> pdb=" O GLN C 479 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL C 484 " --> pdb=" O ALA C 480 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE C 491 " --> pdb=" O GLN C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.986A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 519 removed outlier: 3.515A pdb=" N TYR C 515 " --> pdb=" O LEU C 512 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE C 519 " --> pdb=" O THR C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 559 removed outlier: 3.607A pdb=" N LEU C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER C 559 " --> pdb=" O LEU C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 606 removed outlier: 3.661A pdb=" N ALA C 596 " --> pdb=" O SER C 592 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE C 605 " --> pdb=" O PHE C 601 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY C 606 " --> pdb=" O LYS C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 651 removed outlier: 3.574A pdb=" N ASN C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 672 removed outlier: 3.921A pdb=" N TRP C 660 " --> pdb=" O SER C 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 88 removed outlier: 4.291A pdb=" N SER B 85 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ARG B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.877A pdb=" N THR B 93 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY B 94 " --> pdb=" O GLU B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 94' Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.520A pdb=" N ASP B 108 " --> pdb=" O TYR B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.575A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 135 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.966A pdb=" N VAL B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 229 removed outlier: 3.633A pdb=" N VAL B 226 " --> pdb=" O GLN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 257 removed outlier: 3.703A pdb=" N ALA B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 279 removed outlier: 3.563A pdb=" N ALA B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.834A pdb=" N GLU B 289 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 286 through 290' Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 375 through 389 removed outlier: 4.264A pdb=" N LEU B 381 " --> pdb=" O PRO B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 414 removed outlier: 3.720A pdb=" N PHE B 397 " --> pdb=" O PHE B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 442 removed outlier: 3.729A pdb=" N HIS B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 439 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE B 441 " --> pdb=" O GLY B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 459 removed outlier: 4.038A pdb=" N TYR B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 448 " --> pdb=" O GLY B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 removed outlier: 3.615A pdb=" N TRP B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 460 through 465' Processing helix chain 'B' and resid 470 through 473 Processing helix chain 'B' and resid 474 through 492 Processing helix chain 'B' and resid 497 through 511 Processing helix chain 'B' and resid 512 through 518 removed outlier: 3.829A pdb=" N THR B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 527 removed outlier: 3.875A pdb=" N TYR B 525 " --> pdb=" O THR B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.677A pdb=" N ILE B 533 " --> pdb=" O ILE B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 559 Processing helix chain 'B' and resid 593 through 603 removed outlier: 3.798A pdb=" N PHE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 651 removed outlier: 3.747A pdb=" N VAL B 622 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 674 removed outlier: 3.721A pdb=" N TRP B 660 " --> pdb=" O SER B 656 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS B 661 " --> pdb=" O TRP B 657 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY B 674 " --> pdb=" O GLU B 670 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 331 removed outlier: 3.629A pdb=" N PHE A 330 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 162 through 163 Processing sheet with id=AA3, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.792A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 329 through 331 Processing sheet with id=AA5, first strand: chain 'C' and resid 674 through 675 Processing sheet with id=AA6, first strand: chain 'B' and resid 329 through 331 removed outlier: 3.953A pdb=" N PHE B 330 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR B 343 " --> pdb=" O PHE B 705 " (cutoff:3.500A) 846 hydrogen bonds defined for protein. 2442 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: 5.92 Time building geometry restraints manager: 7.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5552 1.34 - 1.46: 3228 1.46 - 1.57: 10508 1.57 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 19460 Sorted by residual: bond pdb=" CA SER B 504 " pdb=" CB SER B 504 " ideal model delta sigma weight residual 1.529 1.477 0.052 1.55e-02 4.16e+03 1.13e+01 bond pdb=" CA SER D 656 " pdb=" CB SER D 656 " ideal model delta sigma weight residual 1.532 1.486 0.047 1.53e-02 4.27e+03 9.41e+00 bond pdb=" N SER D 656 " pdb=" CA SER D 656 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.27e-02 6.20e+03 3.23e+00 bond pdb=" C SER B 504 " pdb=" O SER B 504 " ideal model delta sigma weight residual 1.236 1.216 0.020 1.15e-02 7.56e+03 3.07e+00 bond pdb=" N SER B 504 " pdb=" CA SER B 504 " ideal model delta sigma weight residual 1.459 1.480 -0.020 1.19e-02 7.06e+03 2.93e+00 ... (remaining 19455 not shown) Histogram of bond angle deviations from ideal: 100.25 - 107.01: 480 107.01 - 113.76: 10849 113.76 - 120.52: 7818 120.52 - 127.27: 7009 127.27 - 134.02: 256 Bond angle restraints: 26412 Sorted by residual: angle pdb=" C SER B 592 " pdb=" CA SER B 592 " pdb=" CB SER B 592 " ideal model delta sigma weight residual 116.54 110.38 6.16 1.15e+00 7.56e-01 2.87e+01 angle pdb=" C ARG C 591 " pdb=" CA ARG C 591 " pdb=" CB ARG C 591 " ideal model delta sigma weight residual 117.23 110.06 7.17 1.36e+00 5.41e-01 2.78e+01 angle pdb=" C PHE C 467 " pdb=" CA PHE C 467 " pdb=" CB PHE C 467 " ideal model delta sigma weight residual 116.54 110.53 6.01 1.15e+00 7.56e-01 2.73e+01 angle pdb=" C TYR C 98 " pdb=" CA TYR C 98 " pdb=" CB TYR C 98 " ideal model delta sigma weight residual 117.23 110.55 6.68 1.36e+00 5.41e-01 2.41e+01 angle pdb=" C SER B 166 " pdb=" CA SER B 166 " pdb=" CB SER B 166 " ideal model delta sigma weight residual 116.34 110.34 6.00 1.40e+00 5.10e-01 1.84e+01 ... (remaining 26407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 10649 17.34 - 34.67: 578 34.67 - 52.01: 132 52.01 - 69.35: 16 69.35 - 86.68: 5 Dihedral angle restraints: 11380 sinusoidal: 4524 harmonic: 6856 Sorted by residual: dihedral pdb=" CA LEU C 345 " pdb=" C LEU C 345 " pdb=" N SER C 346 " pdb=" CA SER C 346 " ideal model delta harmonic sigma weight residual 180.00 159.51 20.49 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LEU D 345 " pdb=" C LEU D 345 " pdb=" N SER D 346 " pdb=" CA SER D 346 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA LEU A 345 " pdb=" C LEU A 345 " pdb=" N SER A 346 " pdb=" CA SER A 346 " ideal model delta harmonic sigma weight residual 180.00 161.88 18.12 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 11377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1838 0.028 - 0.056: 829 0.056 - 0.084: 239 0.084 - 0.113: 89 0.113 - 0.141: 9 Chirality restraints: 3004 Sorted by residual: chirality pdb=" CA THR C 112 " pdb=" N THR C 112 " pdb=" C THR C 112 " pdb=" CB THR C 112 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA MET B 137 " pdb=" N MET B 137 " pdb=" C MET B 137 " pdb=" CB MET B 137 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA ILE C 290 " pdb=" N ILE C 290 " pdb=" C ILE C 290 " pdb=" CB ILE C 290 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.53e-01 ... (remaining 3001 not shown) Planarity restraints: 3236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 137 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO B 138 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 138 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 138 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 232 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO C 233 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 233 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 233 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 366 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO B 367 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 367 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 367 " -0.018 5.00e-02 4.00e+02 ... (remaining 3233 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2948 2.76 - 3.29: 18295 3.29 - 3.83: 29311 3.83 - 4.36: 32023 4.36 - 4.90: 57426 Nonbonded interactions: 140003 Sorted by model distance: nonbonded pdb=" OH TYR A 271 " pdb=" OE2 GLU A 288 " model vdw 2.223 2.440 nonbonded pdb=" O PHE D 519 " pdb=" OG1 THR D 522 " model vdw 2.232 2.440 nonbonded pdb=" O ALA C 124 " pdb=" ND2 ASN C 133 " model vdw 2.249 2.520 nonbonded pdb=" O LEU A 216 " pdb=" OG1 THR A 220 " model vdw 2.252 2.440 nonbonded pdb=" O ALA A 361 " pdb=" NH2 ARG A 369 " model vdw 2.260 2.520 ... (remaining 139998 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' selection = chain 'C' selection = chain 'D' } 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: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 10.560 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 48.540 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.002 0.052 19460 Z= 0.153 Angle : 0.515 7.553 26412 Z= 0.298 Chirality : 0.036 0.141 3004 Planarity : 0.003 0.039 3236 Dihedral : 11.151 86.684 6948 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.47 % Favored : 92.40 % Rotamer: Outliers : 2.73 % Allowed : 6.77 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.19), residues: 2304 helix: 1.33 (0.16), residues: 1208 sheet: -2.77 (0.58), residues: 70 loop : -2.38 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 657 HIS 0.003 0.001 HIS C 363 PHE 0.014 0.001 PHE D 311 TYR 0.010 0.001 TYR C 403 ARG 0.004 0.000 ARG D 490 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 315 time to evaluate : 2.220 Fit side-chains revert: symmetry clash REVERT: A 647 GLU cc_start: 0.8020 (mp0) cc_final: 0.7718 (mp0) REVERT: D 77 ARG cc_start: 0.7266 (mmp80) cc_final: 0.6499 (mmm160) REVERT: C 245 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8857 (tt) REVERT: C 339 ARG cc_start: 0.6932 (mmt180) cc_final: 0.6617 (mmt180) REVERT: C 384 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7525 (tm-30) REVERT: C 467 PHE cc_start: 0.6871 (OUTLIER) cc_final: 0.6405 (t80) REVERT: C 473 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7975 (mm-30) REVERT: C 623 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7890 (tt) REVERT: C 636 LEU cc_start: 0.8942 (tp) cc_final: 0.8703 (tt) REVERT: B 143 ASP cc_start: 0.7897 (t70) cc_final: 0.7479 (t0) REVERT: B 407 PHE cc_start: 0.5070 (OUTLIER) cc_final: 0.4386 (t80) REVERT: B 491 PHE cc_start: 0.5460 (OUTLIER) cc_final: 0.4069 (t80) REVERT: B 593 ILE cc_start: 0.8716 (pt) cc_final: 0.8502 (mt) REVERT: B 640 MET cc_start: 0.8973 (tmm) cc_final: 0.8595 (tmm) REVERT: B 644 LEU cc_start: 0.9043 (mp) cc_final: 0.8732 (mp) REVERT: B 671 MET cc_start: 0.8281 (mtm) cc_final: 0.7955 (mtm) REVERT: B 672 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7321 (tm-30) REVERT: B 687 ARG cc_start: 0.7053 (ptp90) cc_final: 0.6626 (mtm-85) outliers start: 56 outliers final: 14 residues processed: 362 average time/residue: 0.3223 time to fit residues: 175.6928 Evaluate side-chains 245 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 225 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 538 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.8980 chunk 175 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 HIS C 639 ASN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19460 Z= 0.307 Angle : 0.612 11.124 26412 Z= 0.304 Chirality : 0.039 0.143 3004 Planarity : 0.004 0.041 3236 Dihedral : 5.619 58.077 2585 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.77 % Favored : 91.06 % Rotamer: Outliers : 3.61 % Allowed : 10.23 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.18), residues: 2304 helix: 1.37 (0.16), residues: 1228 sheet: -2.84 (0.57), residues: 69 loop : -2.52 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 333 HIS 0.008 0.001 HIS C 363 PHE 0.020 0.002 PHE C 601 TYR 0.018 0.002 TYR C 629 ARG 0.005 0.000 ARG D 490 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 251 time to evaluate : 2.082 Fit side-chains revert: symmetry clash REVERT: D 77 ARG cc_start: 0.7353 (mmp80) cc_final: 0.6423 (mmm160) REVERT: C 245 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8865 (tt) REVERT: C 270 MET cc_start: 0.8678 (tpt) cc_final: 0.8408 (tpt) REVERT: C 384 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7673 (tm-30) REVERT: C 467 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6660 (t80) REVERT: C 473 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8029 (mm-30) REVERT: C 540 PHE cc_start: 0.8133 (t80) cc_final: 0.7915 (t80) REVERT: C 545 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8441 (mm) REVERT: C 636 LEU cc_start: 0.8918 (tp) cc_final: 0.8714 (tt) REVERT: B 137 MET cc_start: 0.8729 (ptt) cc_final: 0.8466 (ptp) REVERT: B 407 PHE cc_start: 0.5079 (OUTLIER) cc_final: 0.4327 (t80) REVERT: B 491 PHE cc_start: 0.5741 (OUTLIER) cc_final: 0.4238 (t80) REVERT: B 593 ILE cc_start: 0.8806 (pt) cc_final: 0.8518 (mt) REVERT: B 672 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7305 (tm-30) REVERT: B 687 ARG cc_start: 0.7150 (ptp90) cc_final: 0.6707 (mtm-85) outliers start: 74 outliers final: 41 residues processed: 307 average time/residue: 0.2803 time to fit residues: 135.4789 Evaluate side-chains 276 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 229 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 363 HIS Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 676 TRP Chi-restraints excluded: chain B residue 689 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 143 optimal weight: 0.9980 chunk 58 optimal weight: 20.0000 chunk 211 optimal weight: 0.8980 chunk 228 optimal weight: 0.9980 chunk 187 optimal weight: 6.9990 chunk 209 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 655 ASN C 521 HIS B 133 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19460 Z= 0.161 Angle : 0.547 13.355 26412 Z= 0.266 Chirality : 0.037 0.241 3004 Planarity : 0.003 0.041 3236 Dihedral : 5.460 55.441 2584 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.07 % Favored : 91.80 % Rotamer: Outliers : 2.83 % Allowed : 13.11 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.19), residues: 2304 helix: 1.63 (0.16), residues: 1227 sheet: -2.79 (0.56), residues: 72 loop : -2.44 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 351 HIS 0.009 0.001 HIS C 521 PHE 0.016 0.001 PHE B 540 TYR 0.016 0.001 TYR C 629 ARG 0.003 0.000 ARG D 490 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 240 time to evaluate : 1.970 Fit side-chains revert: symmetry clash REVERT: D 77 ARG cc_start: 0.7303 (mmp80) cc_final: 0.6302 (mmm160) REVERT: D 121 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8598 (tt) REVERT: C 245 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8870 (tt) REVERT: C 270 MET cc_start: 0.8650 (tpt) cc_final: 0.8428 (tpt) REVERT: C 384 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7596 (tm-30) REVERT: C 467 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6731 (t80) REVERT: C 540 PHE cc_start: 0.8054 (t80) cc_final: 0.7848 (t80) REVERT: C 545 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8377 (mm) REVERT: B 137 MET cc_start: 0.8687 (ptt) cc_final: 0.8426 (ptp) REVERT: B 407 PHE cc_start: 0.5013 (OUTLIER) cc_final: 0.4431 (t80) REVERT: B 491 PHE cc_start: 0.5687 (OUTLIER) cc_final: 0.4247 (t80) REVERT: B 593 ILE cc_start: 0.8762 (pt) cc_final: 0.8490 (mt) REVERT: B 672 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7360 (tm-30) REVERT: B 687 ARG cc_start: 0.7093 (ptp90) cc_final: 0.6594 (mtm-85) outliers start: 58 outliers final: 35 residues processed: 285 average time/residue: 0.3131 time to fit residues: 138.3445 Evaluate side-chains 265 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 224 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 365 LYS Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 642 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 211 optimal weight: 0.4980 chunk 224 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 60 optimal weight: 30.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19460 Z= 0.243 Angle : 0.581 14.726 26412 Z= 0.283 Chirality : 0.038 0.210 3004 Planarity : 0.004 0.043 3236 Dihedral : 5.315 53.764 2579 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.90 % Favored : 90.97 % Rotamer: Outliers : 3.70 % Allowed : 13.21 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.19), residues: 2304 helix: 1.60 (0.16), residues: 1218 sheet: -2.40 (0.60), residues: 68 loop : -2.45 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 464 HIS 0.006 0.001 HIS C 363 PHE 0.023 0.001 PHE C 601 TYR 0.017 0.001 TYR C 412 ARG 0.004 0.000 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 234 time to evaluate : 2.439 Fit side-chains REVERT: A 224 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7278 (p0) REVERT: A 234 HIS cc_start: 0.6763 (p90) cc_final: 0.6430 (p90) REVERT: D 77 ARG cc_start: 0.7342 (mmp80) cc_final: 0.6353 (mmm160) REVERT: D 121 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8638 (tp) REVERT: C 270 MET cc_start: 0.8638 (tpt) cc_final: 0.8381 (tpt) REVERT: C 384 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7657 (tm-30) REVERT: C 467 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.6825 (t80) REVERT: B 137 MET cc_start: 0.8740 (ptt) cc_final: 0.8508 (ptp) REVERT: B 407 PHE cc_start: 0.5087 (OUTLIER) cc_final: 0.4537 (t80) REVERT: B 491 PHE cc_start: 0.5774 (OUTLIER) cc_final: 0.4446 (t80) REVERT: B 531 LYS cc_start: 0.7854 (pttt) cc_final: 0.7175 (tppt) REVERT: B 590 TYR cc_start: 0.6876 (t80) cc_final: 0.6570 (t80) REVERT: B 593 ILE cc_start: 0.8799 (pt) cc_final: 0.8525 (mt) REVERT: B 672 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7343 (tm-30) REVERT: B 687 ARG cc_start: 0.7101 (ptp90) cc_final: 0.6644 (mtm-85) outliers start: 76 outliers final: 48 residues processed: 296 average time/residue: 0.2942 time to fit residues: 136.7774 Evaluate side-chains 277 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 224 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 363 HIS Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 642 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 3 optimal weight: 30.0000 chunk 166 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 114 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 530 GLN B 396 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 19460 Z= 0.372 Angle : 0.665 16.140 26412 Z= 0.326 Chirality : 0.041 0.192 3004 Planarity : 0.004 0.045 3236 Dihedral : 5.337 52.442 2573 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.72 % Favored : 90.02 % Rotamer: Outliers : 4.92 % Allowed : 13.60 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.18), residues: 2304 helix: 1.34 (0.16), residues: 1218 sheet: -2.52 (0.62), residues: 67 loop : -2.58 (0.18), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 464 HIS 0.010 0.001 HIS C 363 PHE 0.019 0.002 PHE B 394 TYR 0.018 0.002 TYR C 471 ARG 0.005 0.000 ARG C 684 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 224 time to evaluate : 2.154 Fit side-chains REVERT: A 224 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7398 (p0) REVERT: A 234 HIS cc_start: 0.6866 (p90) cc_final: 0.6501 (p90) REVERT: D 77 ARG cc_start: 0.7441 (mmp80) cc_final: 0.6365 (mmm160) REVERT: D 468 MET cc_start: 0.6319 (ttp) cc_final: 0.6063 (mmp) REVERT: D 530 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8185 (tp-100) REVERT: C 270 MET cc_start: 0.8666 (tpt) cc_final: 0.8377 (tpt) REVERT: C 384 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7741 (tm-30) REVERT: C 467 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.6899 (t80) REVERT: B 407 PHE cc_start: 0.5286 (OUTLIER) cc_final: 0.4636 (t80) REVERT: B 491 PHE cc_start: 0.6009 (OUTLIER) cc_final: 0.4650 (t80) REVERT: B 590 TYR cc_start: 0.7088 (t80) cc_final: 0.6884 (t80) REVERT: B 672 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7364 (tm-30) outliers start: 101 outliers final: 63 residues processed: 309 average time/residue: 0.2817 time to fit residues: 137.7621 Evaluate side-chains 284 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 216 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 676 TRP Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 363 HIS Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 530 GLN Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 715 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 0.8980 chunk 201 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 224 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 117 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 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 ASN B 396 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19460 Z= 0.156 Angle : 0.573 16.316 26412 Z= 0.272 Chirality : 0.037 0.174 3004 Planarity : 0.003 0.043 3236 Dihedral : 4.940 52.936 2573 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.94 % Favored : 91.80 % Rotamer: Outliers : 3.07 % Allowed : 16.33 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.19), residues: 2304 helix: 1.72 (0.16), residues: 1223 sheet: -2.41 (0.61), residues: 69 loop : -2.48 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP A 464 HIS 0.003 0.001 HIS D 363 PHE 0.028 0.001 PHE C 601 TYR 0.019 0.001 TYR C 629 ARG 0.005 0.000 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 234 time to evaluate : 1.683 Fit side-chains REVERT: A 123 LYS cc_start: 0.8484 (mppt) cc_final: 0.7958 (mmtp) REVERT: A 234 HIS cc_start: 0.6786 (p90) cc_final: 0.6427 (p90) REVERT: D 77 ARG cc_start: 0.7384 (mmp80) cc_final: 0.6274 (mmm160) REVERT: C 384 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7638 (tm-30) REVERT: C 645 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8257 (ttm) REVERT: B 407 PHE cc_start: 0.5163 (OUTLIER) cc_final: 0.4632 (t80) REVERT: B 491 PHE cc_start: 0.5829 (OUTLIER) cc_final: 0.4527 (t80) REVERT: B 645 MET cc_start: 0.8467 (tpp) cc_final: 0.7940 (mmm) REVERT: B 672 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7314 (tm-30) REVERT: B 687 ARG cc_start: 0.7119 (ptp90) cc_final: 0.6683 (mtm-85) outliers start: 63 outliers final: 41 residues processed: 288 average time/residue: 0.2948 time to fit residues: 132.5092 Evaluate side-chains 266 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 222 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 642 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 223 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 530 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 19460 Z= 0.346 Angle : 0.655 17.407 26412 Z= 0.317 Chirality : 0.040 0.177 3004 Planarity : 0.004 0.044 3236 Dihedral : 5.013 48.339 2569 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.24 % Favored : 90.49 % Rotamer: Outliers : 3.46 % Allowed : 16.62 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.18), residues: 2304 helix: 1.45 (0.16), residues: 1221 sheet: -2.62 (0.60), residues: 69 loop : -2.54 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 464 HIS 0.009 0.001 HIS C 363 PHE 0.017 0.002 PHE B 394 TYR 0.026 0.002 TYR A 228 ARG 0.005 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 235 time to evaluate : 1.955 Fit side-chains revert: symmetry clash REVERT: A 123 LYS cc_start: 0.8530 (mppt) cc_final: 0.8011 (mmtp) REVERT: A 224 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7329 (p0) REVERT: A 234 HIS cc_start: 0.6778 (p90) cc_final: 0.6400 (p90) REVERT: D 77 ARG cc_start: 0.7464 (mmp80) cc_final: 0.6380 (mmm160) REVERT: D 143 ASP cc_start: 0.8110 (p0) cc_final: 0.7261 (t0) REVERT: D 468 MET cc_start: 0.6308 (ttp) cc_final: 0.6038 (mmp) REVERT: D 530 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7930 (tp-100) REVERT: C 384 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7741 (tm-30) REVERT: C 645 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8181 (ttm) REVERT: B 407 PHE cc_start: 0.5361 (OUTLIER) cc_final: 0.4774 (t80) REVERT: B 491 PHE cc_start: 0.6008 (OUTLIER) cc_final: 0.4830 (t80) REVERT: B 593 ILE cc_start: 0.8834 (pt) cc_final: 0.8577 (mt) REVERT: B 645 MET cc_start: 0.8569 (tpp) cc_final: 0.8043 (mmm) REVERT: B 672 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7341 (tm-30) outliers start: 71 outliers final: 57 residues processed: 296 average time/residue: 0.3053 time to fit residues: 142.0980 Evaluate side-chains 283 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 221 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 676 TRP Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 530 GLN Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 642 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 152 optimal weight: 0.4980 chunk 110 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 203 optimal weight: 0.6980 chunk 214 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19460 Z= 0.154 Angle : 0.581 17.510 26412 Z= 0.275 Chirality : 0.037 0.165 3004 Planarity : 0.003 0.043 3236 Dihedral : 4.596 49.537 2567 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.03 % Favored : 91.71 % Rotamer: Outliers : 2.78 % Allowed : 17.79 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.19), residues: 2304 helix: 1.72 (0.16), residues: 1229 sheet: -2.36 (0.60), residues: 69 loop : -2.50 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP A 464 HIS 0.004 0.001 HIS D 363 PHE 0.029 0.001 PHE C 601 TYR 0.021 0.001 TYR C 629 ARG 0.004 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 235 time to evaluate : 2.108 Fit side-chains revert: symmetry clash REVERT: A 123 LYS cc_start: 0.8499 (mppt) cc_final: 0.7934 (mmtp) REVERT: A 234 HIS cc_start: 0.6739 (p90) cc_final: 0.6358 (p90) REVERT: D 77 ARG cc_start: 0.7350 (mmp80) cc_final: 0.6183 (mmm160) REVERT: D 468 MET cc_start: 0.6237 (ttp) cc_final: 0.6006 (mmp) REVERT: C 384 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7652 (tm-30) REVERT: C 473 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7567 (mt-10) REVERT: B 491 PHE cc_start: 0.5930 (OUTLIER) cc_final: 0.4688 (t80) REVERT: B 593 ILE cc_start: 0.8806 (pt) cc_final: 0.8549 (mt) REVERT: B 645 MET cc_start: 0.8600 (tpp) cc_final: 0.7972 (mmm) REVERT: B 672 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7328 (tm-30) outliers start: 57 outliers final: 45 residues processed: 284 average time/residue: 0.2935 time to fit residues: 129.7911 Evaluate side-chains 271 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 225 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 642 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.6980 chunk 208 optimal weight: 0.0040 chunk 214 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 207 optimal weight: 0.0030 chunk 136 optimal weight: 0.0970 overall best weight: 0.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 673 ASN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 19460 Z= 0.126 Angle : 0.566 17.395 26412 Z= 0.265 Chirality : 0.037 0.194 3004 Planarity : 0.003 0.041 3236 Dihedral : 4.185 50.157 2564 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.73 % Favored : 92.06 % Rotamer: Outliers : 2.53 % Allowed : 18.13 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.19), residues: 2304 helix: 1.94 (0.16), residues: 1231 sheet: -2.26 (0.60), residues: 70 loop : -2.40 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP A 464 HIS 0.004 0.000 HIS D 363 PHE 0.013 0.001 PHE D 519 TYR 0.019 0.001 TYR C 629 ARG 0.004 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 236 time to evaluate : 2.038 Fit side-chains REVERT: A 123 LYS cc_start: 0.8559 (mppt) cc_final: 0.8004 (mmtp) REVERT: A 224 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7430 (p0) REVERT: D 77 ARG cc_start: 0.7354 (mmp80) cc_final: 0.6224 (mmm160) REVERT: C 384 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7601 (tm-30) REVERT: C 545 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8269 (mm) REVERT: B 141 GLN cc_start: 0.8481 (mp10) cc_final: 0.8240 (mp10) REVERT: B 491 PHE cc_start: 0.5968 (OUTLIER) cc_final: 0.4608 (t80) REVERT: B 645 MET cc_start: 0.8454 (tpp) cc_final: 0.8012 (mmm) REVERT: B 672 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7312 (tm-30) outliers start: 52 outliers final: 42 residues processed: 282 average time/residue: 0.2927 time to fit residues: 128.0207 Evaluate side-chains 265 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 220 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 642 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 0.4980 chunk 134 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 231 optimal weight: 0.0970 chunk 212 optimal weight: 5.9990 chunk 184 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 19460 Z= 0.143 Angle : 0.588 17.951 26412 Z= 0.274 Chirality : 0.037 0.186 3004 Planarity : 0.003 0.041 3236 Dihedral : 4.173 49.647 2564 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.99 % Favored : 91.80 % Rotamer: Outliers : 2.29 % Allowed : 18.71 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.19), residues: 2304 helix: 1.99 (0.16), residues: 1230 sheet: -2.37 (0.59), residues: 72 loop : -2.34 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP A 464 HIS 0.003 0.001 HIS D 363 PHE 0.029 0.001 PHE C 601 TYR 0.019 0.001 TYR C 335 ARG 0.004 0.000 ARG B 687 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 225 time to evaluate : 2.176 Fit side-chains REVERT: A 123 LYS cc_start: 0.8537 (mppt) cc_final: 0.7988 (mmtp) REVERT: D 77 ARG cc_start: 0.7341 (mmp80) cc_final: 0.6175 (mmm160) REVERT: C 384 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7639 (tm-30) REVERT: B 141 GLN cc_start: 0.8473 (mp10) cc_final: 0.8240 (mp10) REVERT: B 491 PHE cc_start: 0.6046 (OUTLIER) cc_final: 0.4689 (t80) REVERT: B 593 ILE cc_start: 0.8766 (pt) cc_final: 0.8495 (mt) REVERT: B 645 MET cc_start: 0.8492 (tpp) cc_final: 0.8036 (mmm) REVERT: B 672 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7333 (tm-30) outliers start: 47 outliers final: 43 residues processed: 265 average time/residue: 0.2958 time to fit residues: 123.5200 Evaluate side-chains 264 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 220 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 642 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 2.9990 chunk 56 optimal weight: 0.0000 chunk 169 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 189 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 overall best weight: 1.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 GLN B 683 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.169168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119787 restraints weight = 29975.668| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.16 r_work: 0.3258 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19460 Z= 0.243 Angle : 0.639 18.399 26412 Z= 0.302 Chirality : 0.039 0.176 3004 Planarity : 0.003 0.042 3236 Dihedral : 4.483 48.253 2562 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.51 % Favored : 91.23 % Rotamer: Outliers : 2.68 % Allowed : 18.71 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.19), residues: 2304 helix: 1.76 (0.16), residues: 1231 sheet: -2.37 (0.59), residues: 72 loop : -2.44 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP A 464 HIS 0.006 0.001 HIS C 363 PHE 0.015 0.001 PHE B 394 TYR 0.023 0.001 TYR C 335 ARG 0.005 0.000 ARG D 490 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4129.98 seconds wall clock time: 75 minutes 39.54 seconds (4539.54 seconds total)