Starting phenix.real_space_refine on Sat Sep 28 10:25:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjh_14748/09_2024/7zjh_14748.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjh_14748/09_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_14748/09_2024/7zjh_14748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjh_14748/09_2024/7zjh_14748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjh_14748/09_2024/7zjh_14748.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjh_14748/09_2024/7zjh_14748.cif" } 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. Time to flip 24 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 10.98, per 1000 atoms: 0.58 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 - 3.00 Amino acid : True - 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: 4.67 Conformation dependent library (CDL) restraints added in 2.3 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: 1.83 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: 5.72 Time building geometry restraints manager: 5.19 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: 0.00 - 1.51: 25929 1.51 - 3.02: 384 3.02 - 4.53: 73 4.53 - 6.04: 21 6.04 - 7.55: 5 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 3.040 nonbonded pdb=" O PHE D 519 " pdb=" OG1 THR D 522 " model vdw 2.232 3.040 nonbonded pdb=" O ALA C 124 " pdb=" ND2 ASN C 133 " model vdw 2.249 3.120 nonbonded pdb=" O LEU A 216 " pdb=" OG1 THR A 220 " model vdw 2.252 3.040 nonbonded pdb=" O ALA A 361 " pdb=" NH2 ARG A 369 " model vdw 2.260 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 40.530 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.100 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.580 ------------------------------------------------------------------------------- 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 : 2.069 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: 0.3060 time to fit residues: 167.3007 Evaluate side-chains 245 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 225 time to evaluate : 2.064 ------------------------------------------------------------------------------- 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: 0.9990 chunk 175 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 118 optimal weight: 0.4980 chunk 93 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN 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: 0.7932 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19460 Z= 0.165 Angle : 0.548 10.085 26412 Z= 0.272 Chirality : 0.037 0.142 3004 Planarity : 0.004 0.043 3236 Dihedral : 5.359 58.730 2585 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.68 % Favored : 92.19 % Rotamer: Outliers : 2.78 % Allowed : 10.43 % Favored : 86.79 % 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: -0.28 (0.19), residues: 2304 helix: 1.55 (0.16), residues: 1235 sheet: -2.58 (0.58), residues: 70 loop : -2.38 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 464 HIS 0.005 0.001 HIS A 683 PHE 0.022 0.001 PHE C 601 TYR 0.017 0.001 TYR C 629 ARG 0.003 0.000 ARG B 684 *********************** 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 308 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 251 time to evaluate : 2.397 Fit side-chains revert: symmetry clash REVERT: D 77 ARG cc_start: 0.7304 (mmp80) cc_final: 0.6444 (mmm160) REVERT: D 143 ASP cc_start: 0.8212 (p0) cc_final: 0.7549 (t0) REVERT: C 245 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8860 (tt) REVERT: C 270 MET cc_start: 0.8693 (tpt) cc_final: 0.8486 (tpt) REVERT: C 384 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7546 (tm-30) REVERT: C 467 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6230 (t80) REVERT: C 473 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7978 (mm-30) REVERT: C 540 PHE cc_start: 0.7986 (t80) cc_final: 0.7763 (t80) REVERT: C 545 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8343 (mm) REVERT: C 636 LEU cc_start: 0.8868 (tp) cc_final: 0.8640 (tt) REVERT: B 137 MET cc_start: 0.8687 (ptt) cc_final: 0.8425 (ptp) REVERT: B 407 PHE cc_start: 0.5012 (OUTLIER) cc_final: 0.4445 (t80) REVERT: B 491 PHE cc_start: 0.5587 (OUTLIER) cc_final: 0.4105 (t80) REVERT: B 593 ILE cc_start: 0.8805 (pt) cc_final: 0.8558 (mt) REVERT: B 672 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7277 (tm-30) REVERT: B 687 ARG cc_start: 0.7010 (ptp90) cc_final: 0.6580 (mtm-85) outliers start: 57 outliers final: 28 residues processed: 293 average time/residue: 0.2805 time to fit residues: 130.9995 Evaluate side-chains 257 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 223 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 433 MET 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 190 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 224 ASP 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 C residue 224 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 292 ASN Chi-restraints excluded: chain B residue 365 LYS 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 0.4980 chunk 65 optimal weight: 0.0270 chunk 175 optimal weight: 10.0000 chunk 143 optimal weight: 0.9980 chunk 58 optimal weight: 20.0000 chunk 211 optimal weight: 8.9990 chunk 228 optimal weight: 0.8980 chunk 187 optimal weight: 20.0000 chunk 209 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 169 optimal weight: 2.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 ASN C 639 ASN B 133 ASN B 650 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19460 Z= 0.137 Angle : 0.541 13.844 26412 Z= 0.262 Chirality : 0.037 0.237 3004 Planarity : 0.003 0.041 3236 Dihedral : 5.230 58.948 2581 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.29 % Favored : 92.58 % Rotamer: Outliers : 2.49 % Allowed : 11.40 % Favored : 86.11 % 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: -0.08 (0.19), residues: 2304 helix: 1.75 (0.16), residues: 1229 sheet: -2.38 (0.58), residues: 72 loop : -2.33 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 351 HIS 0.012 0.001 HIS C 521 PHE 0.016 0.001 PHE B 540 TYR 0.014 0.001 TYR B 455 ARG 0.006 0.000 ARG C 339 *********************** 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 297 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 246 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 HIS cc_start: 0.6659 (p90) cc_final: 0.6347 (p90) REVERT: A 258 ASP cc_start: 0.8123 (t0) cc_final: 0.7816 (t0) REVERT: A 528 MET cc_start: 0.7204 (mmm) cc_final: 0.6619 (mmm) REVERT: D 77 ARG cc_start: 0.7327 (mmp80) cc_final: 0.6360 (mmm160) REVERT: D 143 ASP cc_start: 0.8161 (p0) cc_final: 0.7522 (t0) REVERT: C 245 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8847 (tt) REVERT: C 270 MET cc_start: 0.8657 (tpt) cc_final: 0.8448 (tpt) REVERT: C 384 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7519 (tm-30) REVERT: C 467 PHE cc_start: 0.6976 (OUTLIER) cc_final: 0.6146 (t80) REVERT: C 473 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7902 (mm-30) REVERT: C 540 PHE cc_start: 0.7978 (t80) cc_final: 0.7752 (t80) REVERT: C 545 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8326 (mm) REVERT: C 619 ARG cc_start: 0.6857 (ptt90) cc_final: 0.6653 (mtm180) REVERT: C 636 LEU cc_start: 0.8870 (tp) cc_final: 0.8654 (tt) REVERT: B 407 PHE cc_start: 0.4992 (OUTLIER) cc_final: 0.4444 (t80) REVERT: B 491 PHE cc_start: 0.5582 (OUTLIER) cc_final: 0.4135 (t80) REVERT: B 593 ILE cc_start: 0.8776 (pt) cc_final: 0.8505 (mt) REVERT: B 672 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7314 (tm-30) REVERT: B 687 ARG cc_start: 0.7009 (ptp90) cc_final: 0.6572 (mtm-85) outliers start: 51 outliers final: 27 residues processed: 286 average time/residue: 0.2978 time to fit residues: 132.7274 Evaluate side-chains 260 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 227 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 190 VAL 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 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 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 593 ILE Chi-restraints excluded: chain C residue 224 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 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 292 ASN 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 538 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: 10.0000 chunk 158 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 0.0000 chunk 141 optimal weight: 7.9990 chunk 211 optimal weight: 0.4980 chunk 224 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 200 optimal weight: 0.0070 chunk 60 optimal weight: 30.0000 overall best weight: 0.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 530 GLN B 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19460 Z= 0.128 Angle : 0.521 10.593 26412 Z= 0.254 Chirality : 0.036 0.164 3004 Planarity : 0.003 0.041 3236 Dihedral : 5.128 59.983 2581 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.51 % Favored : 92.36 % Rotamer: Outliers : 3.02 % Allowed : 12.09 % Favored : 84.89 % 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: 0.08 (0.19), residues: 2304 helix: 1.87 (0.16), residues: 1232 sheet: -2.00 (0.60), residues: 72 loop : -2.29 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 464 HIS 0.003 0.000 HIS D 363 PHE 0.026 0.001 PHE C 601 TYR 0.016 0.001 TYR D 525 ARG 0.006 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: 62 poor density : 248 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 LYS cc_start: 0.8472 (mtpp) cc_final: 0.7864 (mtpp) REVERT: A 258 ASP cc_start: 0.8096 (t0) cc_final: 0.7779 (t0) REVERT: D 143 ASP cc_start: 0.8116 (p0) cc_final: 0.7459 (t0) REVERT: D 644 LEU cc_start: 0.9117 (mt) cc_final: 0.8747 (mp) REVERT: C 245 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8821 (tt) REVERT: C 270 MET cc_start: 0.8648 (tpt) cc_final: 0.8416 (tpt) REVERT: C 339 ARG cc_start: 0.6333 (mmt180) cc_final: 0.6042 (mmt180) REVERT: C 384 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7526 (tm-30) REVERT: C 467 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.6154 (t80) REVERT: C 545 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8318 (mm) REVERT: C 636 LEU cc_start: 0.8863 (tp) cc_final: 0.8638 (tt) REVERT: B 407 PHE cc_start: 0.4968 (OUTLIER) cc_final: 0.4447 (t80) REVERT: B 491 PHE cc_start: 0.5610 (OUTLIER) cc_final: 0.4185 (t80) REVERT: B 593 ILE cc_start: 0.8790 (pt) cc_final: 0.8540 (mt) REVERT: B 687 ARG cc_start: 0.7073 (ptp90) cc_final: 0.6638 (mtm-85) outliers start: 62 outliers final: 36 residues processed: 297 average time/residue: 0.2913 time to fit residues: 135.0936 Evaluate side-chains 270 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 229 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 266 LEU 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 638 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 659 ILE 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 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 642 ILE Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 245 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 604 THR Chi-restraints excluded: chain C residue 644 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 365 LYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 538 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: 0.0970 chunk 127 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 166 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 114 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN D 530 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19460 Z= 0.281 Angle : 0.611 8.981 26412 Z= 0.301 Chirality : 0.039 0.182 3004 Planarity : 0.004 0.042 3236 Dihedral : 5.186 57.421 2576 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.38 % Favored : 91.49 % Rotamer: Outliers : 3.51 % Allowed : 12.87 % Favored : 83.63 % 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: -0.22 (0.18), residues: 2304 helix: 1.62 (0.16), residues: 1229 sheet: -2.10 (0.60), residues: 72 loop : -2.40 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 464 HIS 0.007 0.001 HIS C 363 PHE 0.032 0.002 PHE B 549 TYR 0.022 0.002 TYR A 228 ARG 0.006 0.000 ARG D 490 *********************** 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 301 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 229 time to evaluate : 2.081 Fit side-chains revert: symmetry clash REVERT: A 224 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7285 (p0) REVERT: A 234 HIS cc_start: 0.6743 (p90) cc_final: 0.6405 (p90) REVERT: D 77 ARG cc_start: 0.7368 (mmp80) cc_final: 0.6450 (mmm160) REVERT: D 468 MET cc_start: 0.6361 (OUTLIER) cc_final: 0.6013 (mmp) REVERT: D 530 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7925 (tp-100) REVERT: C 192 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8897 (pp) REVERT: C 245 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8837 (tt) REVERT: C 270 MET cc_start: 0.8636 (tpt) cc_final: 0.8342 (tpt) REVERT: C 384 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7628 (tm-30) REVERT: C 467 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6508 (t80) REVERT: C 540 PHE cc_start: 0.8092 (t80) cc_final: 0.7862 (t80) REVERT: C 636 LEU cc_start: 0.8906 (tp) cc_final: 0.8690 (tt) REVERT: B 407 PHE cc_start: 0.4991 (OUTLIER) cc_final: 0.4379 (t80) REVERT: B 491 PHE cc_start: 0.5802 (OUTLIER) cc_final: 0.4448 (t80) REVERT: B 549 PHE cc_start: 0.6710 (t80) cc_final: 0.6395 (t80) REVERT: B 590 TYR cc_start: 0.6941 (t80) cc_final: 0.6673 (t80) REVERT: B 593 ILE cc_start: 0.8851 (pt) cc_final: 0.8557 (mt) REVERT: B 672 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7314 (tm-30) REVERT: B 687 ARG cc_start: 0.7149 (ptp90) cc_final: 0.6622 (mtm-85) outliers start: 72 outliers final: 42 residues processed: 287 average time/residue: 0.2828 time to fit residues: 128.0015 Evaluate side-chains 264 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 214 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 363 HIS Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 468 MET 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 C residue 192 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 245 LEU 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 604 THR 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 310 ILE Chi-restraints excluded: chain B residue 365 LYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 453 LEU 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 538 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 676 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 224 optimal weight: 0.8980 chunk 186 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 650 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19460 Z= 0.181 Angle : 0.571 11.494 26412 Z= 0.277 Chirality : 0.038 0.274 3004 Planarity : 0.004 0.056 3236 Dihedral : 4.981 59.004 2574 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.03 % Favored : 91.80 % Rotamer: Outliers : 3.17 % Allowed : 14.18 % Favored : 82.65 % 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: -0.11 (0.19), residues: 2304 helix: 1.74 (0.16), residues: 1228 sheet: -2.05 (0.60), residues: 72 loop : -2.39 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 464 HIS 0.004 0.001 HIS C 363 PHE 0.023 0.001 PHE B 549 TYR 0.018 0.001 TYR C 629 ARG 0.011 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 291 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 226 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7338 (p0) REVERT: A 234 HIS cc_start: 0.6708 (p90) cc_final: 0.6374 (p90) REVERT: D 266 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8427 (tp) REVERT: D 468 MET cc_start: 0.6363 (OUTLIER) cc_final: 0.5859 (mmp) REVERT: C 192 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8846 (pp) REVERT: C 245 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8852 (tt) REVERT: C 270 MET cc_start: 0.8635 (tpt) cc_final: 0.8391 (tpt) REVERT: C 384 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7596 (tm-30) REVERT: C 467 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.6434 (t80) REVERT: C 540 PHE cc_start: 0.8027 (t80) cc_final: 0.7781 (t80) REVERT: C 545 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8358 (mm) REVERT: C 636 LEU cc_start: 0.8914 (tp) cc_final: 0.8702 (tt) REVERT: B 141 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8208 (mp10) REVERT: B 407 PHE cc_start: 0.5041 (OUTLIER) cc_final: 0.4443 (t80) REVERT: B 491 PHE cc_start: 0.5760 (OUTLIER) cc_final: 0.4380 (t80) REVERT: B 593 ILE cc_start: 0.8840 (pt) cc_final: 0.8542 (mt) REVERT: B 687 ARG cc_start: 0.7129 (ptp90) cc_final: 0.6633 (mtm-85) outliers start: 65 outliers final: 40 residues processed: 281 average time/residue: 0.2900 time to fit residues: 128.6440 Evaluate side-chains 263 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 213 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE 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 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 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 266 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 468 MET 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 192 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 245 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 604 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 141 GLN 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 365 LYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 453 LEU 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 638 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 715 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 136 optimal weight: 0.0470 chunk 103 optimal weight: 7.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 650 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19460 Z= 0.170 Angle : 0.578 17.087 26412 Z= 0.277 Chirality : 0.038 0.361 3004 Planarity : 0.003 0.041 3236 Dihedral : 4.809 56.576 2572 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.20 % Favored : 91.62 % Rotamer: Outliers : 2.88 % Allowed : 15.30 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.19), residues: 2304 helix: 1.80 (0.16), residues: 1232 sheet: -2.07 (0.59), residues: 72 loop : -2.39 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 464 HIS 0.003 0.001 HIS C 363 PHE 0.016 0.001 PHE B 540 TYR 0.032 0.001 TYR B 471 ARG 0.005 0.000 ARG C 339 *********************** 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 288 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 229 time to evaluate : 2.128 Fit side-chains revert: symmetry clash REVERT: A 123 LYS cc_start: 0.8525 (mppt) cc_final: 0.8020 (mmtp) REVERT: A 224 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7407 (p0) REVERT: A 234 HIS cc_start: 0.6626 (p90) cc_final: 0.6267 (p90) REVERT: A 270 MET cc_start: 0.8594 (mmm) cc_final: 0.8379 (mmm) REVERT: D 468 MET cc_start: 0.6355 (OUTLIER) cc_final: 0.5840 (mmp) REVERT: C 192 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8823 (pp) REVERT: C 245 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8832 (tt) REVERT: C 270 MET cc_start: 0.8630 (tpt) cc_final: 0.8401 (tpt) REVERT: C 339 ARG cc_start: 0.6627 (mmt180) cc_final: 0.6411 (mmt180) REVERT: C 384 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7598 (tm-30) REVERT: C 540 PHE cc_start: 0.8041 (t80) cc_final: 0.7785 (t80) REVERT: C 636 LEU cc_start: 0.8931 (tp) cc_final: 0.8727 (tt) REVERT: B 141 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8206 (mp10) REVERT: B 407 PHE cc_start: 0.5110 (OUTLIER) cc_final: 0.4515 (t80) REVERT: B 491 PHE cc_start: 0.5734 (OUTLIER) cc_final: 0.4389 (t80) REVERT: B 593 ILE cc_start: 0.8816 (pt) cc_final: 0.8512 (mt) REVERT: B 672 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7372 (tm-30) REVERT: B 687 ARG cc_start: 0.7127 (ptp90) cc_final: 0.6711 (mtm-85) outliers start: 59 outliers final: 36 residues processed: 277 average time/residue: 0.2831 time to fit residues: 123.0877 Evaluate side-chains 260 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 217 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE 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 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 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 373 VAL Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 468 MET 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 593 ILE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 141 GLN 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 365 LYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 407 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 538 LEU 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: 0.8980 chunk 133 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 chunk 214 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19460 Z= 0.166 Angle : 0.581 16.778 26412 Z= 0.278 Chirality : 0.038 0.382 3004 Planarity : 0.003 0.041 3236 Dihedral : 4.604 55.368 2569 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.94 % Favored : 91.88 % Rotamer: Outliers : 2.68 % Allowed : 15.30 % Favored : 82.02 % 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: 0.01 (0.19), residues: 2304 helix: 1.87 (0.16), residues: 1229 sheet: -2.00 (0.60), residues: 72 loop : -2.38 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 464 HIS 0.003 0.001 HIS C 363 PHE 0.016 0.001 PHE B 540 TYR 0.018 0.001 TYR C 629 ARG 0.003 0.000 ARG D 490 *********************** 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 282 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 227 time to evaluate : 2.076 Fit side-chains revert: symmetry clash REVERT: A 123 LYS cc_start: 0.8521 (mppt) cc_final: 0.7978 (mmtp) REVERT: A 224 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7383 (p0) REVERT: A 234 HIS cc_start: 0.6640 (p90) cc_final: 0.6273 (p90) REVERT: D 468 MET cc_start: 0.6304 (OUTLIER) cc_final: 0.5792 (mmp) REVERT: C 245 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8830 (tt) REVERT: C 270 MET cc_start: 0.8626 (tpt) cc_final: 0.8399 (tpt) REVERT: C 384 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7589 (tm-30) REVERT: C 467 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6270 (t80) REVERT: C 540 PHE cc_start: 0.8039 (t80) cc_final: 0.7800 (t80) REVERT: B 141 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8208 (mp10) REVERT: B 491 PHE cc_start: 0.5848 (OUTLIER) cc_final: 0.4502 (t80) REVERT: B 593 ILE cc_start: 0.8796 (pt) cc_final: 0.8472 (mt) REVERT: B 672 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7386 (tm-30) REVERT: B 687 ARG cc_start: 0.7176 (ptp90) cc_final: 0.6712 (mtm-85) outliers start: 55 outliers final: 37 residues processed: 274 average time/residue: 0.2851 time to fit residues: 121.5832 Evaluate side-chains 266 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 223 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE 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 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 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 373 VAL Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 468 MET 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 593 ILE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 245 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 604 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 141 GLN 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 365 LYS 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 538 LEU 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: 1.9990 chunk 208 optimal weight: 8.9990 chunk 214 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 188 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 207 optimal weight: 8.9990 chunk 136 optimal weight: 0.0370 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19460 Z= 0.171 Angle : 0.608 17.777 26412 Z= 0.285 Chirality : 0.038 0.374 3004 Planarity : 0.003 0.041 3236 Dihedral : 4.480 55.044 2567 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.07 % Favored : 91.75 % Rotamer: Outliers : 2.49 % Allowed : 15.84 % Favored : 81.68 % 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: -0.01 (0.19), residues: 2304 helix: 1.83 (0.16), residues: 1237 sheet: -2.02 (0.60), residues: 72 loop : -2.41 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP A 464 HIS 0.004 0.001 HIS C 363 PHE 0.013 0.001 PHE D 519 TYR 0.017 0.001 TYR C 335 ARG 0.004 0.000 ARG C 339 *********************** 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 280 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 229 time to evaluate : 2.145 Fit side-chains revert: symmetry clash REVERT: A 123 LYS cc_start: 0.8517 (mppt) cc_final: 0.7969 (mmtp) REVERT: A 224 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7422 (p0) REVERT: A 234 HIS cc_start: 0.6658 (p90) cc_final: 0.6289 (p90) REVERT: A 607 MET cc_start: 0.5351 (mmm) cc_final: 0.5146 (mmm) REVERT: A 671 MET cc_start: 0.8937 (mtp) cc_final: 0.8715 (mtp) REVERT: D 266 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8375 (tp) REVERT: C 245 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8829 (tt) REVERT: C 270 MET cc_start: 0.8623 (tpt) cc_final: 0.8394 (tpt) REVERT: C 384 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7616 (tm-30) REVERT: C 467 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6247 (t80) REVERT: B 141 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8208 (mp10) REVERT: B 491 PHE cc_start: 0.5871 (OUTLIER) cc_final: 0.4534 (t80) REVERT: B 593 ILE cc_start: 0.8802 (pt) cc_final: 0.8473 (mt) REVERT: B 672 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7376 (tm-30) REVERT: B 687 ARG cc_start: 0.7092 (ptp90) cc_final: 0.6680 (mtm-85) outliers start: 51 outliers final: 40 residues processed: 272 average time/residue: 0.2799 time to fit residues: 118.6580 Evaluate side-chains 269 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 223 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE 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 266 LEU 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 645 MET Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 659 ILE 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 266 LEU 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 593 ILE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 245 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 604 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 141 GLN 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 365 LYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 453 LEU 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 538 LEU 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: 0.7980 chunk 134 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 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: 0.7955 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19460 Z= 0.163 Angle : 0.609 17.855 26412 Z= 0.285 Chirality : 0.038 0.390 3004 Planarity : 0.003 0.042 3236 Dihedral : 4.457 55.038 2567 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.86 % Favored : 91.97 % Rotamer: Outliers : 2.39 % Allowed : 16.03 % Favored : 81.58 % 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: 0.05 (0.19), residues: 2304 helix: 1.90 (0.16), residues: 1230 sheet: -1.97 (0.60), residues: 72 loop : -2.38 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.001 TRP A 464 HIS 0.003 0.001 HIS C 363 PHE 0.020 0.001 PHE B 540 TYR 0.018 0.001 TYR D 629 ARG 0.006 0.000 ARG C 339 ********************** 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 277 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 228 time to evaluate : 2.171 Fit side-chains revert: symmetry clash REVERT: A 123 LYS cc_start: 0.8528 (mppt) cc_final: 0.7971 (mmtp) REVERT: A 224 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7466 (p0) REVERT: A 234 HIS cc_start: 0.6655 (p90) cc_final: 0.6259 (p90) REVERT: A 258 ASP cc_start: 0.8332 (t0) cc_final: 0.8018 (t0) REVERT: A 270 MET cc_start: 0.8601 (mmm) cc_final: 0.8349 (mmm) REVERT: A 671 MET cc_start: 0.8929 (mtp) cc_final: 0.8699 (mtp) REVERT: D 77 ARG cc_start: 0.7390 (mmp80) cc_final: 0.6377 (mmm160) REVERT: D 266 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8381 (tp) REVERT: D 468 MET cc_start: 0.6441 (mtp) cc_final: 0.6133 (mmp) REVERT: D 640 MET cc_start: 0.9123 (tmm) cc_final: 0.8908 (tmm) REVERT: C 245 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8821 (tt) REVERT: C 270 MET cc_start: 0.8621 (tpt) cc_final: 0.8395 (tpt) REVERT: C 384 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7634 (tm-30) REVERT: C 467 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6164 (t80) REVERT: B 491 PHE cc_start: 0.5940 (OUTLIER) cc_final: 0.4596 (t80) REVERT: B 593 ILE cc_start: 0.8800 (pt) cc_final: 0.8482 (mt) REVERT: B 687 ARG cc_start: 0.7057 (ptp90) cc_final: 0.6620 (mtm-85) outliers start: 49 outliers final: 41 residues processed: 269 average time/residue: 0.2911 time to fit residues: 121.4698 Evaluate side-chains 268 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 222 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE 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 266 LEU 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 645 MET Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 659 ILE 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 266 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 390 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 593 ILE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 245 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 604 THR 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 284 THR Chi-restraints excluded: chain B residue 365 LYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 453 LEU 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 538 LEU 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: 3.9990 chunk 56 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 184 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 189 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 161 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN B 683 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.174466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.125351 restraints weight = 30585.193| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.35 r_work: 0.3327 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19460 Z= 0.150 Angle : 0.607 17.762 26412 Z= 0.284 Chirality : 0.038 0.390 3004 Planarity : 0.003 0.042 3236 Dihedral : 4.396 55.698 2567 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.64 % Favored : 92.19 % Rotamer: Outliers : 2.24 % Allowed : 16.47 % Favored : 81.29 % 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: 0.09 (0.19), residues: 2304 helix: 1.94 (0.16), residues: 1229 sheet: -1.89 (0.60), residues: 72 loop : -2.36 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.001 TRP A 464 HIS 0.003 0.000 HIS D 363 PHE 0.013 0.001 PHE D 519 TYR 0.018 0.001 TYR D 629 ARG 0.006 0.000 ARG C 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4160.30 seconds wall clock time: 75 minutes 18.59 seconds (4518.59 seconds total)