Starting phenix.real_space_refine on Sat Sep 28 18:24:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ras_24385/09_2024/7ras_24385.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ras_24385/09_2024/7ras_24385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ras_24385/09_2024/7ras_24385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ras_24385/09_2024/7ras_24385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ras_24385/09_2024/7ras_24385.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ras_24385/09_2024/7ras_24385.cif" } resolution = 3.64 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= 0.026 sd= 0.082 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 116 5.16 5 C 13072 2.51 5 N 3272 2.21 5 O 3540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 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: 20000 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4964 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 596} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'A0O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B, D Time building chain proxies: 11.13, per 1000 atoms: 0.56 Number of scatterers: 20000 At special positions: 0 Unit cell: (136.95, 136.95, 117.86, 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 116 16.00 O 3540 8.00 N 3272 7.00 C 13072 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: 4.48 Conformation dependent library (CDL) restraints added in 2.3 seconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4664 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 4 sheets defined 65.5% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 115 through 129 removed outlier: 3.540A pdb=" N LYS A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 removed outlier: 3.682A pdb=" N ARG A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 removed outlier: 3.528A pdb=" N MET A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.768A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.845A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.776A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.788A pdb=" N ALA A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.638A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.756A pdb=" N ILE A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 354 through 362 removed outlier: 3.692A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.513A pdb=" N MET A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 4.124A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 460 removed outlier: 4.278A pdb=" N PHE A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYR A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 508 removed outlier: 3.648A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 542 removed outlier: 4.133A pdb=" N PHE A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 563 removed outlier: 4.441A pdb=" N ALA A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 570 through 575 removed outlier: 4.268A pdb=" N MET A 574 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 608 removed outlier: 3.510A pdb=" N VAL A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.915A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 633 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 679 removed outlier: 3.572A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 707 removed outlier: 3.827A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 690 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 removed outlier: 3.550A pdb=" N ARG A 712 " --> pdb=" O PRO A 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 129 removed outlier: 3.539A pdb=" N LYS B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 148 removed outlier: 3.682A pdb=" N ARG B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 161 removed outlier: 3.527A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.767A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.845A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.775A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.789A pdb=" N ALA B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.637A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.756A pdb=" N ILE B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 354 through 362 removed outlier: 3.692A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 360 " --> pdb=" O ILE B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.512A pdb=" N MET B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 4.124A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 460 removed outlier: 4.278A pdb=" N PHE B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR B 456 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYR B 460 " --> pdb=" O THR B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 508 removed outlier: 3.648A pdb=" N ILE B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 542 removed outlier: 4.132A pdb=" N PHE B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 563 removed outlier: 4.440A pdb=" N ALA B 549 " --> pdb=" O LYS B 545 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU B 551 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET B 562 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 566 No H-bonds generated for 'chain 'B' and resid 564 through 566' Processing helix chain 'B' and resid 570 through 575 removed outlier: 4.268A pdb=" N MET B 574 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 608 removed outlier: 3.509A pdb=" N VAL B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.915A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 633 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 679 removed outlier: 3.572A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 707 removed outlier: 3.828A pdb=" N ASN B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 685 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 690 " --> pdb=" O LYS B 686 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 715 removed outlier: 3.549A pdb=" N ARG B 712 " --> pdb=" O PRO B 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 129 removed outlier: 3.539A pdb=" N LYS C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 148 removed outlier: 3.682A pdb=" N ARG C 148 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 161 removed outlier: 3.528A pdb=" N MET C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.767A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.846A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.775A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 234 " --> pdb=" O ILE C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 removed outlier: 3.789A pdb=" N ALA C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.638A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.756A pdb=" N ILE C 324 " --> pdb=" O MET C 320 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 354 through 362 removed outlier: 3.692A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 360 " --> pdb=" O ILE C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.513A pdb=" N MET C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 4.124A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 460 removed outlier: 4.278A pdb=" N PHE C 442 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR C 456 " --> pdb=" O ASN C 452 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR C 460 " --> pdb=" O THR C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 508 removed outlier: 3.648A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 542 removed outlier: 4.133A pdb=" N PHE C 526 " --> pdb=" O PHE C 522 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 563 removed outlier: 4.441A pdb=" N ALA C 549 " --> pdb=" O LYS C 545 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 551 " --> pdb=" O TYR C 547 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET C 562 " --> pdb=" O GLY C 558 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 566 No H-bonds generated for 'chain 'C' and resid 564 through 566' Processing helix chain 'C' and resid 570 through 575 removed outlier: 4.268A pdb=" N MET C 574 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 608 removed outlier: 3.509A pdb=" N VAL C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 removed outlier: 3.916A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE C 633 " --> pdb=" O VAL C 629 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 679 removed outlier: 3.573A pdb=" N LEU C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 707 removed outlier: 3.829A pdb=" N ASN C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 685 " --> pdb=" O VAL C 681 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 690 " --> pdb=" O LYS C 686 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 715 removed outlier: 3.548A pdb=" N ARG C 712 " --> pdb=" O PRO C 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 129 removed outlier: 3.540A pdb=" N LYS D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 148 removed outlier: 3.682A pdb=" N ARG D 148 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 161 removed outlier: 3.528A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.768A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.845A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.775A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 234 " --> pdb=" O ILE D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 removed outlier: 3.790A pdb=" N ALA D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.638A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.757A pdb=" N ILE D 324 " --> pdb=" O MET D 320 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 354 through 362 removed outlier: 3.691A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 360 " --> pdb=" O ILE D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 408 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.514A pdb=" N MET D 419 " --> pdb=" O ASN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 4.125A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 460 removed outlier: 4.278A pdb=" N PHE D 442 " --> pdb=" O LYS D 438 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR D 456 " --> pdb=" O ASN D 452 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR D 460 " --> pdb=" O THR D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 508 removed outlier: 3.648A pdb=" N ILE D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 508 " --> pdb=" O ALA D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 542 removed outlier: 4.132A pdb=" N PHE D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 563 removed outlier: 4.441A pdb=" N ALA D 549 " --> pdb=" O LYS D 545 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU D 551 " --> pdb=" O TYR D 547 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 566 No H-bonds generated for 'chain 'D' and resid 564 through 566' Processing helix chain 'D' and resid 570 through 575 removed outlier: 4.268A pdb=" N MET D 574 " --> pdb=" O SER D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 608 removed outlier: 3.509A pdb=" N VAL D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 removed outlier: 3.915A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE D 633 " --> pdb=" O VAL D 629 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 679 removed outlier: 3.572A pdb=" N LEU D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 707 removed outlier: 3.828A pdb=" N ASN D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG D 690 " --> pdb=" O LYS D 686 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 715 removed outlier: 3.549A pdb=" N ARG D 712 " --> pdb=" O PRO D 708 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 382 removed outlier: 5.318A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 377 through 382 removed outlier: 5.317A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 377 through 382 removed outlier: 5.317A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 377 through 382 removed outlier: 5.317A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) 989 hydrogen bonds defined for protein. 2907 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: 5.46 Time building geometry restraints manager: 5.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3216 1.32 - 1.44: 5536 1.44 - 1.56: 11468 1.56 - 1.69: 8 1.69 - 1.81: 196 Bond restraints: 20424 Sorted by residual: bond pdb=" C07 A0O C 902 " pdb=" C12 A0O C 902 " ideal model delta sigma weight residual 1.430 1.647 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C07 A0O A 902 " pdb=" C12 A0O A 902 " ideal model delta sigma weight residual 1.430 1.646 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C07 A0O D 902 " pdb=" C12 A0O D 902 " ideal model delta sigma weight residual 1.430 1.646 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C07 A0O B 902 " pdb=" C12 A0O B 902 " ideal model delta sigma weight residual 1.430 1.646 -0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C07 A0O B 901 " pdb=" C12 A0O B 901 " ideal model delta sigma weight residual 1.430 1.645 -0.215 2.00e-02 2.50e+03 1.16e+02 ... (remaining 20419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.53: 27385 5.53 - 11.06: 211 11.06 - 16.60: 8 16.60 - 22.13: 8 22.13 - 27.66: 8 Bond angle restraints: 27620 Sorted by residual: angle pdb=" C04 A0O D 902 " pdb=" C06 A0O D 902 " pdb=" O01 A0O D 902 " ideal model delta sigma weight residual 117.13 144.79 -27.66 3.00e+00 1.11e-01 8.50e+01 angle pdb=" C04 A0O C 902 " pdb=" C06 A0O C 902 " pdb=" O01 A0O C 902 " ideal model delta sigma weight residual 117.13 144.76 -27.63 3.00e+00 1.11e-01 8.49e+01 angle pdb=" C04 A0O B 902 " pdb=" C06 A0O B 902 " pdb=" O01 A0O B 902 " ideal model delta sigma weight residual 117.13 144.72 -27.59 3.00e+00 1.11e-01 8.46e+01 angle pdb=" C04 A0O B 901 " pdb=" C06 A0O B 901 " pdb=" O01 A0O B 901 " ideal model delta sigma weight residual 117.13 144.72 -27.59 3.00e+00 1.11e-01 8.46e+01 angle pdb=" C04 A0O A 902 " pdb=" C06 A0O A 902 " pdb=" O01 A0O A 902 " ideal model delta sigma weight residual 117.13 144.69 -27.56 3.00e+00 1.11e-01 8.44e+01 ... (remaining 27615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.14: 11136 15.14 - 30.29: 731 30.29 - 45.43: 225 45.43 - 60.57: 24 60.57 - 75.72: 24 Dihedral angle restraints: 12140 sinusoidal: 4964 harmonic: 7176 Sorted by residual: dihedral pdb=" CA ASP B 414 " pdb=" C ASP B 414 " pdb=" N ASN B 415 " pdb=" CA ASN B 415 " ideal model delta harmonic sigma weight residual 180.00 137.79 42.21 0 5.00e+00 4.00e-02 7.13e+01 dihedral pdb=" CA ASP C 414 " pdb=" C ASP C 414 " pdb=" N ASN C 415 " pdb=" CA ASN C 415 " ideal model delta harmonic sigma weight residual 180.00 137.79 42.21 0 5.00e+00 4.00e-02 7.13e+01 dihedral pdb=" CA ASP D 414 " pdb=" C ASP D 414 " pdb=" N ASN D 415 " pdb=" CA ASN D 415 " ideal model delta harmonic sigma weight residual 180.00 137.83 42.17 0 5.00e+00 4.00e-02 7.11e+01 ... (remaining 12137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2011 0.040 - 0.080: 899 0.080 - 0.119: 168 0.119 - 0.159: 46 0.159 - 0.199: 28 Chirality restraints: 3152 Sorted by residual: chirality pdb=" CA GLU B 423 " pdb=" N GLU B 423 " pdb=" C GLU B 423 " pdb=" CB GLU B 423 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA VAL D 154 " pdb=" N VAL D 154 " pdb=" C VAL D 154 " pdb=" CB VAL D 154 " both_signs ideal model delta sigma weight residual False 2.44 2.24 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CA VAL C 154 " pdb=" N VAL C 154 " pdb=" C VAL C 154 " pdb=" CB VAL C 154 " both_signs ideal model delta sigma weight residual False 2.44 2.24 0.20 2.00e-01 2.50e+01 9.74e-01 ... (remaining 3149 not shown) Planarity restraints: 3420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 752 " 0.044 5.00e-02 4.00e+02 6.74e-02 7.28e+00 pdb=" N PRO D 753 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 753 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 753 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 752 " 0.044 5.00e-02 4.00e+02 6.74e-02 7.26e+00 pdb=" N PRO A 753 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 753 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 753 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 752 " -0.044 5.00e-02 4.00e+02 6.72e-02 7.23e+00 pdb=" N PRO C 753 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 753 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 753 " -0.037 5.00e-02 4.00e+02 ... (remaining 3417 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 5827 2.81 - 3.33: 18509 3.33 - 3.85: 31234 3.85 - 4.38: 37045 4.38 - 4.90: 61921 Nonbonded interactions: 154536 Sorted by model distance: nonbonded pdb=" OG1 THR A 399 " pdb=" O ASN A 401 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR D 399 " pdb=" O ASN D 401 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR C 399 " pdb=" O ASN C 401 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR B 399 " pdb=" O ASN B 401 " model vdw 2.284 3.040 nonbonded pdb=" OD1 ASP C 322 " pdb=" OH TYR C 359 " model vdw 2.285 3.040 ... (remaining 154531 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 41.220 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.010 0.217 20424 Z= 0.635 Angle : 1.327 27.659 27620 Z= 0.639 Chirality : 0.048 0.199 3152 Planarity : 0.006 0.067 3420 Dihedral : 11.929 75.715 7476 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.31 % Favored : 93.19 % Rotamer: Outliers : 1.11 % Allowed : 7.41 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.09 (0.09), residues: 2408 helix: -4.23 (0.05), residues: 1464 sheet: -1.41 (0.43), residues: 92 loop : -3.61 (0.15), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 692 HIS 0.011 0.002 HIS A 417 PHE 0.021 0.002 PHE D 261 TYR 0.020 0.003 TYR A 565 ARG 0.013 0.001 ARG D 696 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 466 time to evaluate : 2.228 Fit side-chains REVERT: A 404 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7567 (mt) REVERT: A 418 GLU cc_start: 0.8162 (tp30) cc_final: 0.7841 (tp30) REVERT: A 436 PHE cc_start: 0.7828 (m-10) cc_final: 0.7587 (m-10) REVERT: A 449 PHE cc_start: 0.8080 (t80) cc_final: 0.7834 (t80) REVERT: A 489 PHE cc_start: 0.8454 (t80) cc_final: 0.8179 (t80) REVERT: A 591 LEU cc_start: 0.9324 (mm) cc_final: 0.9101 (pp) REVERT: A 650 TYR cc_start: 0.6730 (m-80) cc_final: 0.6450 (m-80) REVERT: A 695 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8195 (mm-40) REVERT: B 205 ASN cc_start: 0.8430 (m-40) cc_final: 0.7884 (t0) REVERT: B 404 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7713 (mt) REVERT: B 418 GLU cc_start: 0.8065 (tp30) cc_final: 0.7747 (tp30) REVERT: B 449 PHE cc_start: 0.8045 (t80) cc_final: 0.7837 (t80) REVERT: B 489 PHE cc_start: 0.8547 (t80) cc_final: 0.8260 (t80) REVERT: B 550 CYS cc_start: 0.8448 (m) cc_final: 0.7615 (m) REVERT: B 650 TYR cc_start: 0.6843 (m-80) cc_final: 0.6503 (m-80) REVERT: B 669 LEU cc_start: 0.9544 (tp) cc_final: 0.9341 (tt) REVERT: B 695 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8263 (tp40) REVERT: C 404 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7628 (mt) REVERT: C 418 GLU cc_start: 0.8169 (tp30) cc_final: 0.7868 (tp30) REVERT: C 449 PHE cc_start: 0.8094 (t80) cc_final: 0.7834 (t80) REVERT: C 591 LEU cc_start: 0.9322 (mm) cc_final: 0.9085 (pp) REVERT: C 650 TYR cc_start: 0.6653 (m-80) cc_final: 0.6388 (m-80) REVERT: C 695 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8214 (tp40) REVERT: D 404 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7611 (mt) REVERT: D 418 GLU cc_start: 0.8145 (tp30) cc_final: 0.7807 (tp30) REVERT: D 436 PHE cc_start: 0.7808 (m-10) cc_final: 0.7575 (m-10) REVERT: D 449 PHE cc_start: 0.8093 (t80) cc_final: 0.7825 (t80) REVERT: D 489 PHE cc_start: 0.8471 (t80) cc_final: 0.8222 (t80) REVERT: D 550 CYS cc_start: 0.8395 (m) cc_final: 0.7713 (m) REVERT: D 591 LEU cc_start: 0.9309 (mm) cc_final: 0.9085 (pp) REVERT: D 650 TYR cc_start: 0.6776 (m-80) cc_final: 0.6476 (m-80) REVERT: D 695 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8216 (tp40) outliers start: 24 outliers final: 8 residues processed: 490 average time/residue: 0.2957 time to fit residues: 223.3032 Evaluate side-chains 259 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 247 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 404 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.8980 chunk 184 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 221 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 216 GLN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 HIS A 645 GLN A 671 ASN A 735 ASN B 178 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B 645 GLN B 671 ASN B 735 ASN C 178 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 GLN C 671 ASN C 735 ASN D 178 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN D 671 ASN D 735 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20424 Z= 0.245 Angle : 0.735 12.886 27620 Z= 0.366 Chirality : 0.041 0.207 3152 Planarity : 0.005 0.049 3420 Dihedral : 6.829 45.235 2732 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.78 % Favored : 96.05 % Rotamer: Outliers : 3.38 % Allowed : 12.64 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.14), residues: 2408 helix: -1.57 (0.11), residues: 1552 sheet: -0.79 (0.46), residues: 92 loop : -3.42 (0.17), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 493 HIS 0.006 0.001 HIS A 417 PHE 0.013 0.001 PHE C 633 TYR 0.016 0.001 TYR C 321 ARG 0.004 0.001 ARG D 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 339 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 404 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7965 (mt) REVERT: A 411 THR cc_start: 0.8645 (p) cc_final: 0.8435 (t) REVERT: A 418 GLU cc_start: 0.8161 (tp30) cc_final: 0.7850 (tp30) REVERT: A 430 HIS cc_start: 0.7650 (t70) cc_final: 0.7142 (t70) REVERT: A 479 MET cc_start: 0.6270 (mpp) cc_final: 0.5795 (mpp) REVERT: A 493 TRP cc_start: 0.8176 (t-100) cc_final: 0.7810 (t-100) REVERT: A 521 TRP cc_start: 0.7461 (t60) cc_final: 0.6467 (t60) REVERT: A 532 LEU cc_start: 0.8917 (tp) cc_final: 0.8681 (tp) REVERT: A 550 CYS cc_start: 0.7819 (m) cc_final: 0.7490 (m) REVERT: A 574 MET cc_start: 0.8259 (tpp) cc_final: 0.7995 (tpp) REVERT: A 741 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7797 (pm20) REVERT: B 160 HIS cc_start: 0.8206 (m-70) cc_final: 0.7907 (m-70) REVERT: B 221 ILE cc_start: 0.8872 (mm) cc_final: 0.8528 (mt) REVERT: B 404 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7710 (mt) REVERT: B 411 THR cc_start: 0.8605 (p) cc_final: 0.8393 (t) REVERT: B 418 GLU cc_start: 0.8072 (tp30) cc_final: 0.7780 (tp30) REVERT: B 430 HIS cc_start: 0.7537 (t70) cc_final: 0.7047 (t70) REVERT: B 449 PHE cc_start: 0.8079 (t80) cc_final: 0.7864 (t80) REVERT: B 461 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.7052 (t80) REVERT: B 479 MET cc_start: 0.6126 (mpp) cc_final: 0.5632 (mpp) REVERT: B 521 TRP cc_start: 0.7459 (t60) cc_final: 0.6479 (t60) REVERT: B 550 CYS cc_start: 0.7820 (m) cc_final: 0.7616 (m) REVERT: B 574 MET cc_start: 0.8209 (tpp) cc_final: 0.7950 (tpp) REVERT: B 669 LEU cc_start: 0.9384 (tp) cc_final: 0.9152 (tt) REVERT: C 404 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7974 (mt) REVERT: C 411 THR cc_start: 0.8642 (p) cc_final: 0.8434 (t) REVERT: C 418 GLU cc_start: 0.8151 (tp30) cc_final: 0.7847 (tp30) REVERT: C 430 HIS cc_start: 0.7622 (t70) cc_final: 0.7118 (t70) REVERT: C 479 MET cc_start: 0.6254 (mpp) cc_final: 0.5784 (mpp) REVERT: C 521 TRP cc_start: 0.7468 (t60) cc_final: 0.6474 (t60) REVERT: C 532 LEU cc_start: 0.8925 (tp) cc_final: 0.8686 (tp) REVERT: C 550 CYS cc_start: 0.7746 (m) cc_final: 0.7387 (m) REVERT: C 574 MET cc_start: 0.8251 (tpp) cc_final: 0.7994 (tpp) REVERT: D 404 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7948 (mt) REVERT: D 411 THR cc_start: 0.8631 (p) cc_final: 0.8421 (t) REVERT: D 418 GLU cc_start: 0.8148 (tp30) cc_final: 0.7838 (tp30) REVERT: D 430 HIS cc_start: 0.7646 (t70) cc_final: 0.7158 (t70) REVERT: D 479 MET cc_start: 0.6189 (mpp) cc_final: 0.5709 (mpp) REVERT: D 521 TRP cc_start: 0.7455 (t60) cc_final: 0.6456 (t60) REVERT: D 532 LEU cc_start: 0.8947 (tp) cc_final: 0.8745 (tp) REVERT: D 550 CYS cc_start: 0.7807 (m) cc_final: 0.7461 (m) REVERT: D 574 MET cc_start: 0.8238 (tpp) cc_final: 0.7968 (tpp) REVERT: D 741 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7763 (pm20) outliers start: 73 outliers final: 11 residues processed: 402 average time/residue: 0.2825 time to fit residues: 179.4762 Evaluate side-chains 253 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 235 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 741 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain D residue 741 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 184 optimal weight: 9.9990 chunk 150 optimal weight: 0.3980 chunk 61 optimal weight: 20.0000 chunk 221 optimal weight: 7.9990 chunk 239 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 220 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 197 ASN A 452 ASN A 529 GLN B 143 GLN B 197 ASN B 452 ASN B 523 HIS C 143 GLN C 197 ASN C 216 GLN C 452 ASN C 529 GLN D 143 GLN D 197 ASN D 216 GLN D 452 ASN D 529 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20424 Z= 0.201 Angle : 0.661 12.500 27620 Z= 0.326 Chirality : 0.041 0.234 3152 Planarity : 0.004 0.044 3420 Dihedral : 6.181 45.766 2718 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.70 % Favored : 96.18 % Rotamer: Outliers : 3.38 % Allowed : 14.91 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.16), residues: 2408 helix: -0.21 (0.12), residues: 1560 sheet: -0.44 (0.46), residues: 92 loop : -3.32 (0.18), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 493 HIS 0.004 0.001 HIS B 426 PHE 0.027 0.001 PHE A 489 TYR 0.015 0.001 TYR C 451 ARG 0.004 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 265 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.8127 (tp30) cc_final: 0.7889 (tp30) REVERT: A 430 HIS cc_start: 0.7674 (t70) cc_final: 0.6973 (t70) REVERT: A 461 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.6865 (t80) REVERT: A 479 MET cc_start: 0.6145 (mpp) cc_final: 0.5604 (mpp) REVERT: A 521 TRP cc_start: 0.7321 (t60) cc_final: 0.6557 (t60) REVERT: A 532 LEU cc_start: 0.9010 (tp) cc_final: 0.8794 (tp) REVERT: A 550 CYS cc_start: 0.7862 (m) cc_final: 0.7458 (m) REVERT: A 574 MET cc_start: 0.8246 (tpp) cc_final: 0.7958 (tpp) REVERT: A 581 LYS cc_start: 0.9147 (ttpm) cc_final: 0.8297 (tptt) REVERT: A 741 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7787 (pm20) REVERT: B 418 GLU cc_start: 0.8057 (tp30) cc_final: 0.7838 (tp30) REVERT: B 430 HIS cc_start: 0.7565 (t70) cc_final: 0.7049 (t70) REVERT: B 461 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.7166 (t80) REVERT: B 521 TRP cc_start: 0.7387 (t60) cc_final: 0.6619 (t60) REVERT: B 562 MET cc_start: 0.8878 (tpp) cc_final: 0.8066 (tpt) REVERT: B 574 MET cc_start: 0.8172 (tpp) cc_final: 0.7891 (tpp) REVERT: B 581 LYS cc_start: 0.9200 (ttpm) cc_final: 0.8347 (tptt) REVERT: C 418 GLU cc_start: 0.8126 (tp30) cc_final: 0.7907 (tp30) REVERT: C 479 MET cc_start: 0.6190 (mpp) cc_final: 0.5654 (mpp) REVERT: C 521 TRP cc_start: 0.7316 (t60) cc_final: 0.6561 (t60) REVERT: C 532 LEU cc_start: 0.9018 (tp) cc_final: 0.8796 (tp) REVERT: C 550 CYS cc_start: 0.7832 (m) cc_final: 0.7414 (m) REVERT: C 574 MET cc_start: 0.8231 (tpp) cc_final: 0.7940 (tpp) REVERT: C 581 LYS cc_start: 0.9138 (ttpm) cc_final: 0.8303 (tptt) REVERT: D 404 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8032 (mt) REVERT: D 418 GLU cc_start: 0.8125 (tp30) cc_final: 0.7886 (tp30) REVERT: D 430 HIS cc_start: 0.7667 (t70) cc_final: 0.6989 (t70) REVERT: D 461 TYR cc_start: 0.7632 (OUTLIER) cc_final: 0.6886 (t80) REVERT: D 479 MET cc_start: 0.6092 (mpp) cc_final: 0.5544 (mpp) REVERT: D 488 MET cc_start: 0.7459 (tpp) cc_final: 0.7187 (tpp) REVERT: D 521 TRP cc_start: 0.7329 (t60) cc_final: 0.6561 (t60) REVERT: D 532 LEU cc_start: 0.9005 (tp) cc_final: 0.8800 (tp) REVERT: D 550 CYS cc_start: 0.7851 (m) cc_final: 0.7462 (m) REVERT: D 574 MET cc_start: 0.8204 (tpp) cc_final: 0.7906 (tpp) REVERT: D 581 LYS cc_start: 0.9145 (ttpm) cc_final: 0.8308 (tptt) REVERT: D 741 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7763 (pm20) outliers start: 73 outliers final: 20 residues processed: 322 average time/residue: 0.2703 time to fit residues: 139.7369 Evaluate side-chains 251 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 225 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 741 GLU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain D residue 160 HIS Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 741 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 222 optimal weight: 0.9990 chunk 235 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 211 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 452 ASN B 182 ASN B 216 GLN B 410 ASN B 529 GLN C 410 ASN D 410 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20424 Z= 0.251 Angle : 0.634 10.655 27620 Z= 0.320 Chirality : 0.041 0.193 3152 Planarity : 0.004 0.041 3420 Dihedral : 6.185 50.291 2710 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.47 % Allowed : 15.05 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.16), residues: 2408 helix: 0.36 (0.13), residues: 1584 sheet: -0.27 (0.48), residues: 92 loop : -3.36 (0.18), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 493 HIS 0.009 0.001 HIS C 430 PHE 0.027 0.001 PHE B 489 TYR 0.017 0.001 TYR A 321 ARG 0.003 0.000 ARG C 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 244 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9326 (pp) REVERT: A 418 GLU cc_start: 0.8259 (tp30) cc_final: 0.8022 (tp30) REVERT: A 521 TRP cc_start: 0.7269 (t60) cc_final: 0.6521 (t60) REVERT: A 532 LEU cc_start: 0.9055 (tp) cc_final: 0.8842 (tp) REVERT: A 550 CYS cc_start: 0.7814 (m) cc_final: 0.7397 (m) REVERT: A 574 MET cc_start: 0.8239 (tpp) cc_final: 0.8035 (tpp) REVERT: A 741 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: B 139 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9265 (pp) REVERT: B 418 GLU cc_start: 0.8193 (tp30) cc_final: 0.7975 (tp30) REVERT: B 461 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.7115 (t80) REVERT: B 488 MET cc_start: 0.7535 (tpt) cc_final: 0.7165 (tpp) REVERT: B 521 TRP cc_start: 0.7311 (t60) cc_final: 0.6623 (t60) REVERT: B 562 MET cc_start: 0.8871 (tpp) cc_final: 0.8103 (tpt) REVERT: C 404 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7982 (mt) REVERT: C 418 GLU cc_start: 0.8250 (tp30) cc_final: 0.8009 (tp30) REVERT: C 521 TRP cc_start: 0.7276 (t60) cc_final: 0.6530 (t60) REVERT: C 532 LEU cc_start: 0.9059 (tp) cc_final: 0.8837 (tp) REVERT: C 550 CYS cc_start: 0.7745 (m) cc_final: 0.7309 (m) REVERT: D 404 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8182 (mt) REVERT: D 418 GLU cc_start: 0.8254 (tp30) cc_final: 0.8003 (tp30) REVERT: D 461 TYR cc_start: 0.7609 (OUTLIER) cc_final: 0.6820 (t80) REVERT: D 521 TRP cc_start: 0.7270 (t60) cc_final: 0.6516 (t60) REVERT: D 532 LEU cc_start: 0.9052 (tp) cc_final: 0.8839 (tp) REVERT: D 550 CYS cc_start: 0.7786 (m) cc_final: 0.7348 (m) REVERT: D 741 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7727 (pm20) outliers start: 75 outliers final: 32 residues processed: 298 average time/residue: 0.2718 time to fit residues: 130.5936 Evaluate side-chains 241 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 201 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 741 GLU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 741 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.9447 > 50: distance: 68 - 69: 3.545 distance: 70 - 71: 3.584 distance: 71 - 72: 3.636 distance: 72 - 73: 3.205 distance: 74 - 75: 3.478 distance: 75 - 76: 3.941 distance: 76 - 77: 3.663 distance: 81 - 82: 5.822 distance: 83 - 84: 3.179 distance: 85 - 86: 5.322 distance: 86 - 89: 5.297 distance: 87 - 88: 5.464 distance: 89 - 90: 6.457 distance: 90 - 91: 3.497 distance: 90 - 92: 6.663 distance: 93 - 94: 11.805 distance: 94 - 95: 10.807 distance: 94 - 97: 4.298 distance: 95 - 96: 32.374 distance: 95 - 101: 24.953 distance: 97 - 98: 4.259 distance: 98 - 99: 6.779 distance: 98 - 100: 7.492 distance: 101 - 102: 8.720 distance: 102 - 103: 14.075 distance: 102 - 105: 12.047 distance: 103 - 104: 4.515 distance: 104 - 132: 7.666 distance: 105 - 106: 9.800 distance: 105 - 107: 8.604 distance: 106 - 108: 7.914 distance: 109 - 110: 4.002 distance: 110 - 111: 4.509 distance: 110 - 113: 4.387 distance: 111 - 117: 5.446 distance: 112 - 140: 7.556 distance: 113 - 114: 9.644 distance: 114 - 116: 7.487 distance: 118 - 119: 3.322 distance: 118 - 121: 3.772 distance: 119 - 120: 3.503 distance: 121 - 122: 4.906 distance: 122 - 123: 5.332 distance: 122 - 124: 7.379 distance: 123 - 125: 7.314 distance: 124 - 126: 7.182 distance: 125 - 126: 5.195 distance: 127 - 128: 4.386 distance: 128 - 129: 3.833 distance: 128 - 131: 3.717 distance: 129 - 130: 4.507 distance: 129 - 132: 5.462 distance: 130 - 154: 7.866 distance: 133 - 136: 3.391 distance: 136 - 137: 4.442 distance: 137 - 138: 8.545