Starting phenix.real_space_refine on Mon Jul 22 23:14:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rau_24386/07_2024/7rau_24386.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rau_24386/07_2024/7rau_24386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rau_24386/07_2024/7rau_24386.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rau_24386/07_2024/7rau_24386.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rau_24386/07_2024/7rau_24386.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rau_24386/07_2024/7rau_24386.cif" } resolution = 3.99 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= 0.003 sd= 0.021 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 Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 698": "NH1" <-> "NH2" Residue "A ARG 716": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 462": "NH1" <-> "NH2" Residue "B TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 698": "NH1" <-> "NH2" Residue "B ARG 716": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 698": "NH1" <-> "NH2" Residue "C ARG 716": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 319": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 698": "NH1" <-> "NH2" Residue "D ARG 716": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 20000 Number of models: 1 Model: "" Number of chains: 8 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: "B" 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: "C" 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: "D" 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} Chain: "B" 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} Chain: "C" 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} Chain: "D" 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} Time building chain proxies: 10.94, per 1000 atoms: 0.55 Number of scatterers: 20000 At special positions: 0 Unit cell: (144.1, 144.1, 118.8, 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.04 Conformation dependent library (CDL) restraints added in 3.4 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: 116 helices and 4 sheets defined 66.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 115 through 129 Processing helix chain 'A' and resid 131 through 149 removed outlier: 3.529A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 removed outlier: 3.860A pdb=" N MET A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 182 through 198 removed outlier: 4.014A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.752A 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 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 281 Processing helix chain 'A' and resid 293 through 297 removed outlier: 4.262A pdb=" N ASN A 297 " --> pdb=" O SER A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.521A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.877A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.661A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.596A pdb=" N LEU A 370 " --> pdb=" O GLU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.717A pdb=" N MET A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.783A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 458 removed outlier: 3.614A pdb=" N PHE A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 508 removed outlier: 3.647A pdb=" N TRP A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 542 removed outlier: 3.514A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 565 removed outlier: 3.654A pdb=" N TRP A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 569 removed outlier: 3.552A pdb=" N PHE A 569 " --> pdb=" O THR A 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 566 through 569' Processing helix chain 'A' and resid 573 through 607 removed outlier: 3.581A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS A 585 " --> pdb=" O LYS A 581 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.618A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 681 removed outlier: 3.594A pdb=" N LEU A 658 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 670 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 705 removed outlier: 4.626A pdb=" N GLU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 697 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 131 through 149 removed outlier: 3.529A pdb=" N LEU B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 removed outlier: 3.861A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 198 removed outlier: 4.014A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.753A 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 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 281 Processing helix chain 'B' and resid 293 through 297 removed outlier: 4.261A pdb=" N ASN B 297 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.521A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.878A pdb=" N ARG B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.661A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.595A pdb=" N LEU B 370 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.717A pdb=" N MET B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.782A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 458 removed outlier: 3.614A pdb=" N PHE B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 508 removed outlier: 3.646A pdb=" N TRP B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 542 removed outlier: 3.514A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 565 removed outlier: 3.654A pdb=" N TRP B 559 " --> pdb=" O MET B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 569 removed outlier: 3.551A pdb=" N PHE B 569 " --> pdb=" O THR B 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 566 through 569' Processing helix chain 'B' and resid 573 through 607 removed outlier: 3.582A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS B 585 " --> pdb=" O LYS B 581 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE B 601 " --> pdb=" O PHE B 597 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.618A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 681 removed outlier: 3.593A pdb=" N LEU B 658 " --> pdb=" O PHE B 654 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 705 removed outlier: 4.626A pdb=" N GLU B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 715 Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 131 through 149 removed outlier: 3.529A pdb=" N LEU C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 162 removed outlier: 3.862A pdb=" N MET C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 182 through 198 removed outlier: 4.013A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.753A 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 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 281 Processing helix chain 'C' and resid 293 through 297 removed outlier: 4.261A pdb=" N ASN C 297 " --> pdb=" O SER C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.521A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.877A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.660A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 361 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.596A pdb=" N LEU C 370 " --> pdb=" O GLU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.716A pdb=" N MET C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.783A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 458 removed outlier: 3.614A pdb=" N PHE C 442 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 508 removed outlier: 3.647A pdb=" N TRP C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 542 removed outlier: 3.514A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 565 removed outlier: 3.653A pdb=" N TRP C 559 " --> pdb=" O MET C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 569 removed outlier: 3.551A pdb=" N PHE C 569 " --> pdb=" O THR C 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 566 through 569' Processing helix chain 'C' and resid 573 through 607 removed outlier: 3.581A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS C 585 " --> pdb=" O LYS C 581 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE C 601 " --> pdb=" O PHE C 597 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 removed outlier: 3.618A pdb=" N LEU C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 681 removed outlier: 3.593A pdb=" N LEU C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 670 " --> pdb=" O PHE C 666 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 705 removed outlier: 4.626A pdb=" N GLU C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 697 " --> pdb=" O ARG C 693 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 715 Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 131 through 149 removed outlier: 3.529A pdb=" N LEU D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 162 removed outlier: 3.861A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 198 removed outlier: 4.014A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.753A 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 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 281 Processing helix chain 'D' and resid 293 through 297 removed outlier: 4.262A pdb=" N ASN D 297 " --> pdb=" O SER D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.522A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.878A pdb=" N ARG D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 329 " --> pdb=" O LEU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.660A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 361 " --> pdb=" O LEU D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.595A pdb=" N LEU D 370 " --> pdb=" O GLU D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.717A pdb=" N MET D 419 " --> pdb=" O ASN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.782A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 458 removed outlier: 3.614A pdb=" N PHE D 442 " --> pdb=" O LYS D 438 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 508 removed outlier: 3.646A pdb=" N TRP D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS D 496 " --> pdb=" O ILE D 492 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 508 " --> pdb=" O ALA D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 542 removed outlier: 3.515A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 565 removed outlier: 3.653A pdb=" N TRP D 559 " --> pdb=" O MET D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 569 removed outlier: 3.551A pdb=" N PHE D 569 " --> pdb=" O THR D 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 566 through 569' Processing helix chain 'D' and resid 573 through 607 removed outlier: 3.581A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS D 585 " --> pdb=" O LYS D 581 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE D 601 " --> pdb=" O PHE D 597 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 removed outlier: 3.617A pdb=" N LEU D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 681 removed outlier: 3.594A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 670 " --> pdb=" O PHE D 666 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 705 removed outlier: 4.626A pdb=" N GLU D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 715 Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 382 removed outlier: 5.489A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 385 " --> pdb=" O TYR A 382 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A 723 " --> pdb=" O ASP A 727 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 377 through 382 removed outlier: 5.489A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 385 " --> pdb=" O TYR B 382 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL B 723 " --> pdb=" O ASP B 727 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 377 through 382 removed outlier: 5.489A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 385 " --> pdb=" O TYR C 382 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL C 723 " --> pdb=" O ASP C 727 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 377 through 382 removed outlier: 5.489A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL D 385 " --> pdb=" O TYR D 382 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL D 723 " --> pdb=" O ASP D 727 " (cutoff:3.500A) 1049 hydrogen bonds defined for protein. 3111 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: 5.87 Time building geometry restraints manager: 8.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3386 1.32 - 1.44: 5383 1.44 - 1.57: 11451 1.57 - 1.69: 8 1.69 - 1.81: 196 Bond restraints: 20424 Sorted by residual: bond pdb=" C07 A0O D 901 " pdb=" C12 A0O D 901 " ideal model delta sigma weight residual 1.430 1.644 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C07 A0O D 902 " pdb=" C12 A0O D 902 " ideal model delta sigma weight residual 1.430 1.644 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C07 A0O C 902 " pdb=" C12 A0O C 902 " ideal model delta sigma weight residual 1.430 1.644 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C07 A0O C 901 " pdb=" C12 A0O C 901 " ideal model delta sigma weight residual 1.430 1.644 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C07 A0O B 902 " pdb=" C12 A0O B 902 " ideal model delta sigma weight residual 1.430 1.644 -0.214 2.00e-02 2.50e+03 1.14e+02 ... (remaining 20419 not shown) Histogram of bond angle deviations from ideal: 99.34 - 108.39: 761 108.39 - 117.43: 14328 117.43 - 126.48: 12207 126.48 - 135.52: 316 135.52 - 144.57: 8 Bond angle restraints: 27620 Sorted by residual: angle pdb=" C04 A0O A 902 " pdb=" C06 A0O A 902 " pdb=" O01 A0O A 902 " ideal model delta sigma weight residual 117.13 144.57 -27.44 3.00e+00 1.11e-01 8.36e+01 angle pdb=" C04 A0O C 902 " pdb=" C06 A0O C 902 " pdb=" O01 A0O C 902 " ideal model delta sigma weight residual 117.13 144.56 -27.43 3.00e+00 1.11e-01 8.36e+01 angle pdb=" C04 A0O B 902 " pdb=" C06 A0O B 902 " pdb=" O01 A0O B 902 " ideal model delta sigma weight residual 117.13 144.44 -27.31 3.00e+00 1.11e-01 8.29e+01 angle pdb=" C04 A0O D 902 " pdb=" C06 A0O D 902 " pdb=" O01 A0O D 902 " ideal model delta sigma weight residual 117.13 144.43 -27.30 3.00e+00 1.11e-01 8.28e+01 angle pdb=" C04 A0O A 901 " pdb=" C06 A0O A 901 " pdb=" O01 A0O A 901 " ideal model delta sigma weight residual 117.13 144.26 -27.13 3.00e+00 1.11e-01 8.18e+01 ... (remaining 27615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.20: 11032 15.20 - 30.39: 792 30.39 - 45.59: 252 45.59 - 60.79: 44 60.79 - 75.99: 20 Dihedral angle restraints: 12140 sinusoidal: 4964 harmonic: 7176 Sorted by residual: 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 180.00 137.21 42.79 0 5.00e+00 4.00e-02 7.32e+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 180.00 137.23 42.77 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" CA ASP A 414 " pdb=" C ASP A 414 " pdb=" N ASN A 415 " pdb=" CA ASN A 415 " ideal model delta harmonic sigma weight residual 180.00 137.25 42.75 0 5.00e+00 4.00e-02 7.31e+01 ... (remaining 12137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2454 0.056 - 0.112: 621 0.112 - 0.167: 57 0.167 - 0.223: 12 0.223 - 0.279: 8 Chirality restraints: 3152 Sorted by residual: chirality pdb=" CG LEU B 673 " pdb=" CB LEU B 673 " pdb=" CD1 LEU B 673 " pdb=" CD2 LEU B 673 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CG LEU D 673 " pdb=" CB LEU D 673 " pdb=" CD1 LEU D 673 " pdb=" CD2 LEU D 673 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CG LEU C 673 " pdb=" CB LEU C 673 " pdb=" CD1 LEU C 673 " pdb=" CD2 LEU C 673 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 3149 not shown) Planarity restraints: 3420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 314 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.98e+00 pdb=" C ASN C 314 " 0.046 2.00e-02 2.50e+03 pdb=" O ASN C 314 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP C 315 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 314 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C ASN B 314 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN B 314 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP B 315 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 314 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C ASN D 314 " -0.045 2.00e-02 2.50e+03 pdb=" O ASN D 314 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP D 315 " 0.015 2.00e-02 2.50e+03 ... (remaining 3417 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6176 2.82 - 3.34: 19707 3.34 - 3.86: 31987 3.86 - 4.38: 37272 4.38 - 4.90: 59259 Nonbonded interactions: 154401 Sorted by model distance: nonbonded pdb=" OD1 ASN D 180 " pdb=" OG1 THR D 183 " model vdw 2.299 2.440 nonbonded pdb=" OD1 ASN B 180 " pdb=" OG1 THR B 183 " model vdw 2.299 2.440 nonbonded pdb=" OD1 ASN C 180 " pdb=" OG1 THR C 183 " model vdw 2.300 2.440 nonbonded pdb=" OD1 ASN A 180 " pdb=" OG1 THR A 183 " model vdw 2.300 2.440 nonbonded pdb=" O ALA A 604 " pdb=" OG SER A 607 " model vdw 2.310 2.440 ... (remaining 154396 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.100 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: 0.000 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 51.840 Find NCS groups from input model: 1.090 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 : 0.009 0.214 20424 Z= 0.592 Angle : 1.259 27.437 27620 Z= 0.624 Chirality : 0.048 0.279 3152 Planarity : 0.005 0.046 3420 Dihedral : 12.741 75.985 7476 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.31 % Favored : 93.52 % Rotamer: Outliers : 1.11 % Allowed : 6.67 % Favored : 92.22 % 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: -4.28 (0.12), residues: 2408 helix: -3.15 (0.08), residues: 1424 sheet: 2.30 (0.57), residues: 64 loop : -2.43 (0.16), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 559 HIS 0.006 0.002 HIS B 523 PHE 0.021 0.002 PHE D 526 TYR 0.024 0.003 TYR D 213 ARG 0.006 0.001 ARG D 416 *********************** 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 680 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 656 time to evaluate : 2.532 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.9224 (mmp) cc_final: 0.8446 (mmm) REVERT: A 174 LYS cc_start: 0.9484 (tttp) cc_final: 0.8688 (ttpt) REVERT: A 178 ASN cc_start: 0.9478 (m110) cc_final: 0.8902 (p0) REVERT: A 257 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8714 (mt-10) REVERT: A 268 LEU cc_start: 0.9781 (tp) cc_final: 0.9566 (tt) REVERT: A 284 ASN cc_start: 0.9266 (t0) cc_final: 0.9001 (t0) REVERT: A 308 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8817 (tt0) REVERT: A 323 MET cc_start: 0.9138 (tpp) cc_final: 0.8783 (tpp) REVERT: A 333 LEU cc_start: 0.9284 (tp) cc_final: 0.8410 (tp) REVERT: A 355 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8853 (tp30) REVERT: A 364 GLU cc_start: 0.9010 (pp20) cc_final: 0.8723 (tm-30) REVERT: A 392 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9333 (mm) REVERT: A 396 ASP cc_start: 0.8539 (t70) cc_final: 0.8212 (t70) REVERT: A 405 GLU cc_start: 0.9457 (tt0) cc_final: 0.9109 (pt0) REVERT: A 414 ASP cc_start: 0.9122 (t0) cc_final: 0.8879 (p0) REVERT: A 415 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.7803 (t0) REVERT: A 418 GLU cc_start: 0.9556 (tp30) cc_final: 0.9341 (mp0) REVERT: A 419 MET cc_start: 0.9526 (mtm) cc_final: 0.9216 (mtm) REVERT: A 423 GLU cc_start: 0.8199 (tp30) cc_final: 0.7845 (tp30) REVERT: A 438 LYS cc_start: 0.8927 (ptmm) cc_final: 0.8586 (tptt) REVERT: A 440 MET cc_start: 0.9135 (mmp) cc_final: 0.8668 (mmp) REVERT: A 448 TYR cc_start: 0.7606 (t80) cc_final: 0.6368 (t80) REVERT: A 479 MET cc_start: 0.5935 (tpt) cc_final: 0.4912 (tmm) REVERT: A 489 PHE cc_start: 0.9419 (t80) cc_final: 0.9023 (t80) REVERT: A 538 PHE cc_start: 0.8695 (m-10) cc_final: 0.8477 (t80) REVERT: A 547 TYR cc_start: 0.7774 (p90) cc_final: 0.7409 (p90) REVERT: A 562 MET cc_start: 0.9199 (tpt) cc_final: 0.8408 (tpp) REVERT: A 572 MET cc_start: 0.8723 (ppp) cc_final: 0.7956 (tpt) REVERT: A 575 TYR cc_start: 0.8340 (p90) cc_final: 0.7886 (p90) REVERT: A 578 MET cc_start: 0.8717 (mmm) cc_final: 0.8445 (mmm) REVERT: A 597 PHE cc_start: 0.8037 (t80) cc_final: 0.7577 (t80) REVERT: A 702 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8400 (mt-10) REVERT: A 704 GLU cc_start: 0.9259 (tp30) cc_final: 0.8604 (tp30) REVERT: A 734 ILE cc_start: 0.9160 (mt) cc_final: 0.8835 (mm) REVERT: B 159 MET cc_start: 0.9169 (mmp) cc_final: 0.8419 (mmm) REVERT: B 174 LYS cc_start: 0.9430 (tttp) cc_final: 0.8439 (ttpt) REVERT: B 178 ASN cc_start: 0.9270 (m110) cc_final: 0.8573 (p0) REVERT: B 257 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8605 (mt-10) REVERT: B 261 PHE cc_start: 0.9289 (p90) cc_final: 0.8799 (p90) REVERT: B 284 ASN cc_start: 0.9223 (t0) cc_final: 0.8998 (t0) REVERT: B 308 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8697 (tt0) REVERT: B 320 MET cc_start: 0.9023 (mmp) cc_final: 0.8792 (mmt) REVERT: B 323 MET cc_start: 0.9132 (tpp) cc_final: 0.8878 (tpt) REVERT: B 333 LEU cc_start: 0.9134 (tp) cc_final: 0.8283 (tp) REVERT: B 350 LYS cc_start: 0.9451 (tttt) cc_final: 0.9209 (ttmm) REVERT: B 392 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9327 (mm) REVERT: B 396 ASP cc_start: 0.8383 (t70) cc_final: 0.7992 (t70) REVERT: B 405 GLU cc_start: 0.9449 (tt0) cc_final: 0.9095 (pt0) REVERT: B 412 ASN cc_start: 0.9578 (p0) cc_final: 0.9367 (p0) REVERT: B 414 ASP cc_start: 0.9072 (t0) cc_final: 0.8742 (p0) REVERT: B 415 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.7401 (t0) REVERT: B 418 GLU cc_start: 0.9609 (tp30) cc_final: 0.9268 (mp0) REVERT: B 419 MET cc_start: 0.9549 (mtm) cc_final: 0.9304 (mtm) REVERT: B 423 GLU cc_start: 0.8493 (tp30) cc_final: 0.8082 (tp30) REVERT: B 438 LYS cc_start: 0.9050 (ptmm) cc_final: 0.8686 (tptt) REVERT: B 440 MET cc_start: 0.9126 (mmp) cc_final: 0.8695 (mmp) REVERT: B 448 TYR cc_start: 0.7683 (t80) cc_final: 0.6425 (t80) REVERT: B 479 MET cc_start: 0.6227 (tpt) cc_final: 0.5653 (tmm) REVERT: B 489 PHE cc_start: 0.9373 (t80) cc_final: 0.9008 (t80) REVERT: B 562 MET cc_start: 0.9144 (tpt) cc_final: 0.8256 (tpp) REVERT: B 572 MET cc_start: 0.8786 (ppp) cc_final: 0.8056 (tpt) REVERT: B 575 TYR cc_start: 0.8406 (p90) cc_final: 0.7852 (p90) REVERT: B 578 MET cc_start: 0.8551 (mmm) cc_final: 0.8290 (mmm) REVERT: B 597 PHE cc_start: 0.8075 (t80) cc_final: 0.7608 (t80) REVERT: B 695 GLN cc_start: 0.9422 (mt0) cc_final: 0.8489 (tt0) REVERT: B 702 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8501 (mt-10) REVERT: B 704 GLU cc_start: 0.9221 (tp30) cc_final: 0.8962 (tp30) REVERT: C 159 MET cc_start: 0.9175 (mmp) cc_final: 0.8378 (mmm) REVERT: C 174 LYS cc_start: 0.9463 (tttp) cc_final: 0.9067 (tptt) REVERT: C 177 LEU cc_start: 0.9825 (mm) cc_final: 0.9514 (mt) REVERT: C 178 ASN cc_start: 0.9381 (m110) cc_final: 0.8635 (p0) REVERT: C 257 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8600 (mt-10) REVERT: C 261 PHE cc_start: 0.9334 (p90) cc_final: 0.8799 (p90) REVERT: C 268 LEU cc_start: 0.9774 (tp) cc_final: 0.9527 (tt) REVERT: C 284 ASN cc_start: 0.9261 (t0) cc_final: 0.9013 (t0) REVERT: C 290 THR cc_start: 0.9365 (p) cc_final: 0.9150 (t) REVERT: C 308 GLU cc_start: 0.9259 (mm-30) cc_final: 0.8728 (tt0) REVERT: C 320 MET cc_start: 0.9176 (mmp) cc_final: 0.8952 (mmt) REVERT: C 323 MET cc_start: 0.9160 (tpp) cc_final: 0.8956 (tpt) REVERT: C 333 LEU cc_start: 0.9163 (tp) cc_final: 0.8293 (tp) REVERT: C 364 GLU cc_start: 0.9043 (pp20) cc_final: 0.8774 (tm-30) REVERT: C 371 ARG cc_start: 0.8970 (mtp-110) cc_final: 0.8348 (ttm110) REVERT: C 396 ASP cc_start: 0.8467 (t70) cc_final: 0.8136 (t70) REVERT: C 405 GLU cc_start: 0.9448 (tt0) cc_final: 0.9076 (pt0) REVERT: C 414 ASP cc_start: 0.9144 (t0) cc_final: 0.8738 (p0) REVERT: C 415 ASN cc_start: 0.9163 (OUTLIER) cc_final: 0.7935 (t0) REVERT: C 418 GLU cc_start: 0.9597 (tp30) cc_final: 0.9363 (mp0) REVERT: C 419 MET cc_start: 0.9530 (mtm) cc_final: 0.9318 (mtm) REVERT: C 438 LYS cc_start: 0.9067 (ptmm) cc_final: 0.8719 (tptt) REVERT: C 440 MET cc_start: 0.9044 (mmp) cc_final: 0.8563 (mmp) REVERT: C 448 TYR cc_start: 0.7658 (t80) cc_final: 0.7237 (t80) REVERT: C 479 MET cc_start: 0.6170 (tpt) cc_final: 0.5356 (tmm) REVERT: C 489 PHE cc_start: 0.9369 (t80) cc_final: 0.9068 (t80) REVERT: C 572 MET cc_start: 0.8794 (ppp) cc_final: 0.8026 (tpt) REVERT: C 575 TYR cc_start: 0.8304 (p90) cc_final: 0.7876 (p90) REVERT: C 578 MET cc_start: 0.8628 (mmm) cc_final: 0.8324 (mmm) REVERT: C 597 PHE cc_start: 0.8030 (t80) cc_final: 0.7557 (t80) REVERT: C 702 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8495 (mt-10) REVERT: C 704 GLU cc_start: 0.9231 (tp30) cc_final: 0.8978 (tp30) REVERT: D 159 MET cc_start: 0.9068 (mmp) cc_final: 0.8258 (mmm) REVERT: D 174 LYS cc_start: 0.9375 (tttp) cc_final: 0.8983 (tptt) REVERT: D 177 LEU cc_start: 0.9809 (mm) cc_final: 0.9435 (mt) REVERT: D 178 ASN cc_start: 0.9336 (m110) cc_final: 0.8592 (p0) REVERT: D 257 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8632 (mt-10) REVERT: D 261 PHE cc_start: 0.9318 (p90) cc_final: 0.8810 (p90) REVERT: D 268 LEU cc_start: 0.9764 (tp) cc_final: 0.9502 (tt) REVERT: D 284 ASN cc_start: 0.9221 (t0) cc_final: 0.8959 (t0) REVERT: D 290 THR cc_start: 0.9312 (p) cc_final: 0.9104 (t) REVERT: D 308 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8725 (tt0) REVERT: D 320 MET cc_start: 0.9205 (mmp) cc_final: 0.8971 (mmt) REVERT: D 323 MET cc_start: 0.9201 (tpp) cc_final: 0.8844 (tpt) REVERT: D 333 LEU cc_start: 0.9201 (tp) cc_final: 0.8289 (tp) REVERT: D 364 GLU cc_start: 0.9052 (pp20) cc_final: 0.8771 (tm-30) REVERT: D 396 ASP cc_start: 0.8479 (t70) cc_final: 0.8151 (t70) REVERT: D 405 GLU cc_start: 0.9454 (tt0) cc_final: 0.9073 (pt0) REVERT: D 414 ASP cc_start: 0.9191 (t0) cc_final: 0.8758 (p0) REVERT: D 415 ASN cc_start: 0.9157 (OUTLIER) cc_final: 0.7912 (t0) REVERT: D 418 GLU cc_start: 0.9598 (tp30) cc_final: 0.9362 (mp0) REVERT: D 419 MET cc_start: 0.9551 (mtm) cc_final: 0.9333 (mtm) REVERT: D 438 LYS cc_start: 0.8939 (ptmm) cc_final: 0.8634 (tptt) REVERT: D 440 MET cc_start: 0.9093 (mmp) cc_final: 0.8618 (mmp) REVERT: D 448 TYR cc_start: 0.7547 (t80) cc_final: 0.6749 (t80) REVERT: D 479 MET cc_start: 0.5880 (tpt) cc_final: 0.5266 (tmm) REVERT: D 489 PHE cc_start: 0.9381 (t80) cc_final: 0.9052 (t80) REVERT: D 550 CYS cc_start: 0.9324 (m) cc_final: 0.9106 (t) REVERT: D 562 MET cc_start: 0.9161 (tpt) cc_final: 0.8232 (tpp) REVERT: D 572 MET cc_start: 0.8824 (ppp) cc_final: 0.8078 (tpt) REVERT: D 575 TYR cc_start: 0.8302 (p90) cc_final: 0.7763 (p90) REVERT: D 578 MET cc_start: 0.8627 (mmm) cc_final: 0.8296 (mmm) REVERT: D 597 PHE cc_start: 0.7924 (t80) cc_final: 0.7468 (t80) REVERT: D 702 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8368 (mt-10) REVERT: D 704 GLU cc_start: 0.9283 (tp30) cc_final: 0.8699 (tp30) outliers start: 24 outliers final: 0 residues processed: 672 average time/residue: 0.2715 time to fit residues: 288.5062 Evaluate side-chains 473 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 467 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 415 ASN Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain D residue 415 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.7980 chunk 184 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 221 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 244 HIS A 330 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN A 483 GLN A 735 ASN B 160 HIS B 244 HIS B 330 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN B 671 ASN B 735 ASN C 160 HIS C 244 HIS C 330 ASN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 671 ASN C 735 ASN D 160 HIS D 244 HIS D 330 ASN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 ASN D 671 ASN D 735 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20424 Z= 0.195 Angle : 0.715 10.557 27620 Z= 0.369 Chirality : 0.039 0.177 3152 Planarity : 0.004 0.030 3420 Dihedral : 6.490 38.550 2720 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.80 % Allowed : 14.72 % 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: -1.43 (0.15), residues: 2408 helix: -0.48 (0.12), residues: 1544 sheet: 2.19 (0.63), residues: 68 loop : -2.00 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 521 HIS 0.005 0.001 HIS A 426 PHE 0.015 0.001 PHE B 524 TYR 0.015 0.001 TYR B 565 ARG 0.003 0.000 ARG A 375 *********************** 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 587 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 505 time to evaluate : 2.298 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9732 (mt) cc_final: 0.9420 (pp) REVERT: A 178 ASN cc_start: 0.9343 (m110) cc_final: 0.8437 (p0) REVERT: A 257 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8714 (mt-10) REVERT: A 261 PHE cc_start: 0.9380 (p90) cc_final: 0.9052 (p90) REVERT: A 284 ASN cc_start: 0.9148 (t0) cc_final: 0.8904 (t0) REVERT: A 308 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8827 (tt0) REVERT: A 320 MET cc_start: 0.9247 (mmp) cc_final: 0.9034 (mmt) REVERT: A 355 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8874 (tp30) REVERT: A 364 GLU cc_start: 0.9029 (pp20) cc_final: 0.8736 (tm-30) REVERT: A 371 ARG cc_start: 0.9031 (mtp-110) cc_final: 0.8448 (ttm-80) REVERT: A 405 GLU cc_start: 0.9580 (tt0) cc_final: 0.9189 (pt0) REVERT: A 414 ASP cc_start: 0.9070 (t0) cc_final: 0.8707 (p0) REVERT: A 438 LYS cc_start: 0.8921 (ptmm) cc_final: 0.8508 (tptt) REVERT: A 448 TYR cc_start: 0.6971 (t80) cc_final: 0.6059 (t80) REVERT: A 479 MET cc_start: 0.5731 (tpt) cc_final: 0.5029 (ttt) REVERT: A 488 MET cc_start: 0.8564 (mtp) cc_final: 0.8256 (ptp) REVERT: A 542 PHE cc_start: 0.6329 (m-10) cc_final: 0.5857 (m-10) REVERT: A 562 MET cc_start: 0.9227 (tpt) cc_final: 0.8609 (tpp) REVERT: A 572 MET cc_start: 0.8725 (ppp) cc_final: 0.7963 (tpt) REVERT: A 575 TYR cc_start: 0.8059 (p90) cc_final: 0.7626 (p90) REVERT: A 597 PHE cc_start: 0.7763 (t80) cc_final: 0.6657 (t80) REVERT: A 661 TYR cc_start: 0.8899 (t80) cc_final: 0.8606 (t80) REVERT: A 702 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8625 (mt-10) REVERT: A 704 GLU cc_start: 0.9261 (tp30) cc_final: 0.8885 (tm-30) REVERT: A 706 MET cc_start: 0.9204 (mmp) cc_final: 0.8990 (mmm) REVERT: B 139 LEU cc_start: 0.9734 (mt) cc_final: 0.9496 (pp) REVERT: B 174 LYS cc_start: 0.9494 (tttp) cc_final: 0.8653 (ttpt) REVERT: B 178 ASN cc_start: 0.9189 (m110) cc_final: 0.8295 (p0) REVERT: B 214 GLU cc_start: 0.9564 (tm-30) cc_final: 0.8750 (tm-30) REVERT: B 257 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8580 (mt-10) REVERT: B 308 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8726 (tt0) REVERT: B 323 MET cc_start: 0.9205 (tpp) cc_final: 0.8982 (tpt) REVERT: B 405 GLU cc_start: 0.9557 (tt0) cc_final: 0.9088 (pt0) REVERT: B 414 ASP cc_start: 0.8964 (t0) cc_final: 0.8534 (p0) REVERT: B 419 MET cc_start: 0.9369 (mtm) cc_final: 0.9058 (mtm) REVERT: B 438 LYS cc_start: 0.9034 (ptmm) cc_final: 0.8626 (tptt) REVERT: B 448 TYR cc_start: 0.7177 (t80) cc_final: 0.6263 (t80) REVERT: B 479 MET cc_start: 0.5938 (tpt) cc_final: 0.5283 (ttt) REVERT: B 488 MET cc_start: 0.8514 (mtp) cc_final: 0.8271 (ptp) REVERT: B 562 MET cc_start: 0.9166 (tpt) cc_final: 0.8330 (tpt) REVERT: B 572 MET cc_start: 0.8796 (ppp) cc_final: 0.7960 (tpt) REVERT: B 575 TYR cc_start: 0.8113 (p90) cc_final: 0.7336 (p90) REVERT: B 578 MET cc_start: 0.8591 (mmm) cc_final: 0.8286 (mmm) REVERT: B 597 PHE cc_start: 0.7762 (t80) cc_final: 0.6600 (t80) REVERT: B 661 TYR cc_start: 0.8781 (t80) cc_final: 0.8488 (t80) REVERT: B 704 GLU cc_start: 0.9263 (tp30) cc_final: 0.8828 (tm-30) REVERT: C 139 LEU cc_start: 0.9717 (mt) cc_final: 0.9440 (pp) REVERT: C 142 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9326 (tm) REVERT: C 174 LYS cc_start: 0.9547 (tttp) cc_final: 0.8772 (ttpt) REVERT: C 178 ASN cc_start: 0.9277 (m110) cc_final: 0.8380 (p0) REVERT: C 214 GLU cc_start: 0.9542 (tm-30) cc_final: 0.8689 (tm-30) REVERT: C 257 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8614 (mt-10) REVERT: C 261 PHE cc_start: 0.9351 (p90) cc_final: 0.8959 (p90) REVERT: C 284 ASN cc_start: 0.9147 (t0) cc_final: 0.8936 (t0) REVERT: C 290 THR cc_start: 0.9410 (p) cc_final: 0.9149 (t) REVERT: C 308 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8729 (tt0) REVERT: C 323 MET cc_start: 0.9228 (tpp) cc_final: 0.9027 (tpt) REVERT: C 364 GLU cc_start: 0.9055 (pp20) cc_final: 0.8844 (tm-30) REVERT: C 405 GLU cc_start: 0.9523 (tt0) cc_final: 0.9050 (pt0) REVERT: C 414 ASP cc_start: 0.9078 (t0) cc_final: 0.8600 (p0) REVERT: C 419 MET cc_start: 0.9376 (mtm) cc_final: 0.9070 (mtm) REVERT: C 438 LYS cc_start: 0.9085 (ptmm) cc_final: 0.8663 (tptt) REVERT: C 448 TYR cc_start: 0.7688 (t80) cc_final: 0.7304 (t80) REVERT: C 479 MET cc_start: 0.5937 (tpt) cc_final: 0.5268 (ttp) REVERT: C 488 MET cc_start: 0.8483 (mtp) cc_final: 0.8254 (ptp) REVERT: C 493 TRP cc_start: 0.8498 (t60) cc_final: 0.7929 (t60) REVERT: C 572 MET cc_start: 0.8781 (ppp) cc_final: 0.8051 (tpt) REVERT: C 574 MET cc_start: 0.8645 (mmt) cc_final: 0.8272 (mmm) REVERT: C 575 TYR cc_start: 0.8050 (p90) cc_final: 0.7291 (p90) REVERT: C 578 MET cc_start: 0.8581 (mmm) cc_final: 0.8304 (mmm) REVERT: C 597 PHE cc_start: 0.7732 (t80) cc_final: 0.6676 (t80) REVERT: C 661 TYR cc_start: 0.8823 (t80) cc_final: 0.8580 (t80) REVERT: C 704 GLU cc_start: 0.9259 (tp30) cc_final: 0.8823 (tm-30) REVERT: D 139 LEU cc_start: 0.9743 (mt) cc_final: 0.9482 (pp) REVERT: D 174 LYS cc_start: 0.9484 (tttp) cc_final: 0.8648 (ttpt) REVERT: D 178 ASN cc_start: 0.9223 (m110) cc_final: 0.8286 (p0) REVERT: D 214 GLU cc_start: 0.9555 (tm-30) cc_final: 0.8715 (tm-30) REVERT: D 257 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8610 (mt-10) REVERT: D 261 PHE cc_start: 0.9332 (p90) cc_final: 0.8957 (p90) REVERT: D 284 ASN cc_start: 0.9096 (t0) cc_final: 0.8832 (t0) REVERT: D 290 THR cc_start: 0.9380 (p) cc_final: 0.9136 (t) REVERT: D 293 ASP cc_start: 0.8939 (p0) cc_final: 0.8720 (p0) REVERT: D 308 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8760 (tt0) REVERT: D 323 MET cc_start: 0.9260 (tpp) cc_final: 0.8911 (tpt) REVERT: D 336 MET cc_start: 0.8550 (ttm) cc_final: 0.8334 (ttm) REVERT: D 364 GLU cc_start: 0.9074 (pp20) cc_final: 0.8822 (tm-30) REVERT: D 405 GLU cc_start: 0.9526 (tt0) cc_final: 0.9135 (pt0) REVERT: D 410 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8474 (t0) REVERT: D 414 ASP cc_start: 0.9127 (t0) cc_final: 0.8620 (p0) REVERT: D 419 MET cc_start: 0.9392 (mtm) cc_final: 0.9074 (mtm) REVERT: D 438 LYS cc_start: 0.9018 (ptmm) cc_final: 0.8585 (tptt) REVERT: D 448 TYR cc_start: 0.7618 (t80) cc_final: 0.7224 (t80) REVERT: D 479 MET cc_start: 0.5834 (tpt) cc_final: 0.5231 (ttt) REVERT: D 488 MET cc_start: 0.8462 (mtp) cc_final: 0.8258 (ptp) REVERT: D 493 TRP cc_start: 0.8527 (t60) cc_final: 0.7701 (t60) REVERT: D 532 LEU cc_start: 0.9162 (mt) cc_final: 0.8762 (tp) REVERT: D 550 CYS cc_start: 0.9289 (m) cc_final: 0.9069 (m) REVERT: D 572 MET cc_start: 0.8800 (ppp) cc_final: 0.8072 (tpt) REVERT: D 575 TYR cc_start: 0.8148 (p90) cc_final: 0.7371 (p90) REVERT: D 578 MET cc_start: 0.8559 (mmm) cc_final: 0.8280 (mmm) REVERT: D 597 PHE cc_start: 0.7655 (t80) cc_final: 0.6615 (t80) REVERT: D 661 TYR cc_start: 0.8790 (t80) cc_final: 0.8587 (t80) REVERT: D 704 GLU cc_start: 0.9297 (tp30) cc_final: 0.8828 (tm-30) outliers start: 82 outliers final: 34 residues processed: 562 average time/residue: 0.2543 time to fit residues: 232.5700 Evaluate side-chains 467 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 431 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 450 PHE Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 585 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 221 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 197 optimal weight: 8.9990 chunk 220 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 178 optimal weight: 0.0050 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20424 Z= 0.148 Angle : 0.666 10.332 27620 Z= 0.327 Chirality : 0.039 0.183 3152 Planarity : 0.003 0.025 3420 Dihedral : 5.752 36.792 2708 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.78 % Allowed : 18.70 % Favored : 78.52 % 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: -0.27 (0.17), residues: 2408 helix: 0.58 (0.13), residues: 1552 sheet: 2.30 (0.62), residues: 68 loop : -1.91 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 521 HIS 0.004 0.001 HIS D 426 PHE 0.017 0.001 PHE A 489 TYR 0.019 0.001 TYR D 547 ARG 0.003 0.000 ARG A 416 *********************** 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 555 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 495 time to evaluate : 2.560 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9690 (mt) cc_final: 0.9357 (pp) REVERT: A 178 ASN cc_start: 0.9382 (m110) cc_final: 0.8503 (p0) REVERT: A 214 GLU cc_start: 0.9521 (tm-30) cc_final: 0.9231 (tp30) REVERT: A 244 HIS cc_start: 0.8872 (m90) cc_final: 0.8224 (m90) REVERT: A 284 ASN cc_start: 0.9165 (t0) cc_final: 0.8944 (t0) REVERT: A 308 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8750 (tt0) REVERT: A 355 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8864 (tp30) REVERT: A 405 GLU cc_start: 0.9586 (tt0) cc_final: 0.9110 (pt0) REVERT: A 438 LYS cc_start: 0.8856 (ptmm) cc_final: 0.8478 (tptt) REVERT: A 448 TYR cc_start: 0.7263 (t80) cc_final: 0.6553 (t80) REVERT: A 479 MET cc_start: 0.5342 (tpt) cc_final: 0.4616 (ttt) REVERT: A 508 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.5954 (tp) REVERT: A 527 PHE cc_start: 0.9382 (t80) cc_final: 0.9149 (t80) REVERT: A 555 MET cc_start: 0.9235 (mtm) cc_final: 0.8734 (mpp) REVERT: A 562 MET cc_start: 0.9258 (tpt) cc_final: 0.8840 (tpp) REVERT: A 572 MET cc_start: 0.8799 (ppp) cc_final: 0.8093 (tpt) REVERT: A 575 TYR cc_start: 0.8031 (p90) cc_final: 0.7716 (p90) REVERT: A 597 PHE cc_start: 0.7748 (t80) cc_final: 0.7391 (t80) REVERT: A 598 LEU cc_start: 0.8883 (tp) cc_final: 0.8591 (tp) REVERT: A 702 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8646 (mt-10) REVERT: A 704 GLU cc_start: 0.9253 (tp30) cc_final: 0.8946 (tm-30) REVERT: B 139 LEU cc_start: 0.9768 (mt) cc_final: 0.9554 (pp) REVERT: B 174 LYS cc_start: 0.9423 (tttp) cc_final: 0.8616 (ttpt) REVERT: B 178 ASN cc_start: 0.9165 (m110) cc_final: 0.8207 (p0) REVERT: B 214 GLU cc_start: 0.9527 (tm-30) cc_final: 0.8736 (tm-30) REVERT: B 257 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8574 (mt-10) REVERT: B 261 PHE cc_start: 0.9046 (p90) cc_final: 0.8563 (p90) REVERT: B 290 THR cc_start: 0.9394 (p) cc_final: 0.9137 (t) REVERT: B 308 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8721 (tt0) REVERT: B 405 GLU cc_start: 0.9595 (tt0) cc_final: 0.9373 (tt0) REVERT: B 414 ASP cc_start: 0.8879 (t0) cc_final: 0.8625 (p0) REVERT: B 438 LYS cc_start: 0.8975 (ptmm) cc_final: 0.8590 (tptt) REVERT: B 448 TYR cc_start: 0.7405 (t80) cc_final: 0.6864 (t80) REVERT: B 479 MET cc_start: 0.5524 (tpt) cc_final: 0.4885 (ttt) REVERT: B 488 MET cc_start: 0.8483 (mtp) cc_final: 0.8117 (ptp) REVERT: B 508 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.5926 (tp) REVERT: B 572 MET cc_start: 0.8810 (ppp) cc_final: 0.8435 (tmm) REVERT: B 574 MET cc_start: 0.8493 (mmt) cc_final: 0.7857 (mmm) REVERT: B 575 TYR cc_start: 0.8305 (p90) cc_final: 0.8096 (p90) REVERT: B 578 MET cc_start: 0.8598 (mmm) cc_final: 0.8299 (mmm) REVERT: B 704 GLU cc_start: 0.9320 (tp30) cc_final: 0.8997 (tm-30) REVERT: C 139 LEU cc_start: 0.9716 (mt) cc_final: 0.9475 (pp) REVERT: C 174 LYS cc_start: 0.9525 (tttp) cc_final: 0.8733 (ttpt) REVERT: C 178 ASN cc_start: 0.9270 (m110) cc_final: 0.8301 (p0) REVERT: C 214 GLU cc_start: 0.9526 (tm-30) cc_final: 0.8601 (tm-30) REVERT: C 257 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8614 (mt-10) REVERT: C 261 PHE cc_start: 0.9168 (p90) cc_final: 0.8714 (p90) REVERT: C 284 ASN cc_start: 0.9158 (t0) cc_final: 0.8882 (t0) REVERT: C 290 THR cc_start: 0.9378 (p) cc_final: 0.9137 (t) REVERT: C 308 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8721 (tt0) REVERT: C 405 GLU cc_start: 0.9550 (tt0) cc_final: 0.9139 (pt0) REVERT: C 414 ASP cc_start: 0.8932 (t0) cc_final: 0.8648 (p0) REVERT: C 438 LYS cc_start: 0.8986 (ptmm) cc_final: 0.8586 (tptt) REVERT: C 448 TYR cc_start: 0.7840 (t80) cc_final: 0.7381 (t80) REVERT: C 479 MET cc_start: 0.5735 (tpt) cc_final: 0.5060 (ttt) REVERT: C 488 MET cc_start: 0.8439 (mtp) cc_final: 0.8186 (ptp) REVERT: C 508 LEU cc_start: 0.6381 (OUTLIER) cc_final: 0.5785 (tp) REVERT: C 559 TRP cc_start: 0.9309 (m100) cc_final: 0.8555 (m100) REVERT: C 572 MET cc_start: 0.8865 (ppp) cc_final: 0.8188 (tpt) REVERT: C 575 TYR cc_start: 0.8217 (p90) cc_final: 0.7892 (p90) REVERT: C 578 MET cc_start: 0.8611 (mmm) cc_final: 0.8400 (mmm) REVERT: C 672 MET cc_start: 0.8975 (tpp) cc_final: 0.8562 (tpt) REVERT: C 692 TRP cc_start: 0.8756 (t60) cc_final: 0.8244 (t60) REVERT: C 702 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8740 (mt-10) REVERT: C 704 GLU cc_start: 0.9297 (tp30) cc_final: 0.9006 (tm-30) REVERT: D 139 LEU cc_start: 0.9769 (mt) cc_final: 0.9547 (pp) REVERT: D 174 LYS cc_start: 0.9468 (tttp) cc_final: 0.8715 (tttt) REVERT: D 178 ASN cc_start: 0.9208 (m110) cc_final: 0.8261 (p0) REVERT: D 214 GLU cc_start: 0.9531 (tm-30) cc_final: 0.8643 (tm-30) REVERT: D 257 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8600 (mt-10) REVERT: D 261 PHE cc_start: 0.9167 (p90) cc_final: 0.8728 (p90) REVERT: D 284 ASN cc_start: 0.9170 (t0) cc_final: 0.8900 (t0) REVERT: D 290 THR cc_start: 0.9350 (p) cc_final: 0.9062 (t) REVERT: D 308 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8707 (tt0) REVERT: D 336 MET cc_start: 0.8675 (ttm) cc_final: 0.8435 (ttm) REVERT: D 405 GLU cc_start: 0.9585 (tt0) cc_final: 0.9046 (pt0) REVERT: D 414 ASP cc_start: 0.9023 (t0) cc_final: 0.8666 (p0) REVERT: D 438 LYS cc_start: 0.8964 (ptmm) cc_final: 0.8566 (tptt) REVERT: D 448 TYR cc_start: 0.7850 (t80) cc_final: 0.7396 (t80) REVERT: D 479 MET cc_start: 0.5574 (tpt) cc_final: 0.4985 (ttt) REVERT: D 488 MET cc_start: 0.8481 (mtp) cc_final: 0.8264 (ptp) REVERT: D 493 TRP cc_start: 0.8429 (t60) cc_final: 0.7758 (t60) REVERT: D 508 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.5690 (tt) REVERT: D 532 LEU cc_start: 0.9308 (mt) cc_final: 0.8895 (tp) REVERT: D 572 MET cc_start: 0.8830 (ppp) cc_final: 0.8344 (tpt) REVERT: D 578 MET cc_start: 0.8657 (mmm) cc_final: 0.8417 (mmm) REVERT: D 672 MET cc_start: 0.8994 (tpp) cc_final: 0.8600 (tpt) REVERT: D 702 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8724 (mt-10) REVERT: D 704 GLU cc_start: 0.9295 (tp30) cc_final: 0.9059 (tm-30) outliers start: 60 outliers final: 28 residues processed: 537 average time/residue: 0.2637 time to fit residues: 230.6745 Evaluate side-chains 459 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 427 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 171 CYS Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 636 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 222 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20424 Z= 0.218 Angle : 0.683 10.725 27620 Z= 0.342 Chirality : 0.040 0.259 3152 Planarity : 0.003 0.025 3420 Dihedral : 5.690 37.604 2708 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.21 % Allowed : 20.09 % Favored : 75.69 % 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: 0.01 (0.17), residues: 2408 helix: 0.84 (0.13), residues: 1596 sheet: 2.68 (0.58), residues: 64 loop : -2.07 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 493 HIS 0.003 0.001 HIS A 417 PHE 0.018 0.001 PHE D 715 TYR 0.016 0.002 TYR B 547 ARG 0.004 0.000 ARG B 716 *********************** 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 519 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 428 time to evaluate : 2.364 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ASN cc_start: 0.9386 (m110) cc_final: 0.8506 (p0) REVERT: A 244 HIS cc_start: 0.8924 (m90) cc_final: 0.8126 (m90) REVERT: A 261 PHE cc_start: 0.9297 (p90) cc_final: 0.8726 (p90) REVERT: A 284 ASN cc_start: 0.9181 (t0) cc_final: 0.8976 (t0) REVERT: A 290 THR cc_start: 0.9429 (OUTLIER) cc_final: 0.9212 (t) REVERT: A 308 GLU cc_start: 0.9337 (mm-30) cc_final: 0.8720 (tt0) REVERT: A 405 GLU cc_start: 0.9623 (tt0) cc_final: 0.9111 (pt0) REVERT: A 420 LEU cc_start: 0.9776 (OUTLIER) cc_final: 0.9538 (mm) REVERT: A 448 TYR cc_start: 0.7444 (t80) cc_final: 0.6967 (t80) REVERT: A 479 MET cc_start: 0.5140 (tpt) cc_final: 0.4355 (ttt) REVERT: A 488 MET cc_start: 0.8634 (mtp) cc_final: 0.8374 (ptp) REVERT: A 508 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.5879 (tp) REVERT: A 527 PHE cc_start: 0.9386 (t80) cc_final: 0.9151 (t80) REVERT: A 702 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8705 (mt-10) REVERT: A 704 GLU cc_start: 0.9256 (tp30) cc_final: 0.9031 (tm-30) REVERT: B 139 LEU cc_start: 0.9798 (mt) cc_final: 0.9504 (pp) REVERT: B 159 MET cc_start: 0.9060 (mmm) cc_final: 0.8600 (mmm) REVERT: B 174 LYS cc_start: 0.9524 (tttp) cc_final: 0.8728 (ttpt) REVERT: B 178 ASN cc_start: 0.9268 (m110) cc_final: 0.8314 (p0) REVERT: B 214 GLU cc_start: 0.9541 (tm-30) cc_final: 0.9186 (tp30) REVERT: B 253 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.9082 (ttpp) REVERT: B 257 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8638 (mt-10) REVERT: B 261 PHE cc_start: 0.9029 (p90) cc_final: 0.8400 (p90) REVERT: B 290 THR cc_start: 0.9474 (p) cc_final: 0.9244 (t) REVERT: B 308 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8750 (tt0) REVERT: B 405 GLU cc_start: 0.9608 (tt0) cc_final: 0.9206 (pt0) REVERT: B 414 ASP cc_start: 0.9062 (t0) cc_final: 0.8811 (p0) REVERT: B 438 LYS cc_start: 0.8924 (ptmm) cc_final: 0.8536 (tptt) REVERT: B 448 TYR cc_start: 0.7575 (t80) cc_final: 0.6918 (t80) REVERT: B 479 MET cc_start: 0.5295 (tpt) cc_final: 0.4598 (ttt) REVERT: B 508 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.5958 (tp) REVERT: B 555 MET cc_start: 0.9298 (ttm) cc_final: 0.9093 (mmm) REVERT: B 572 MET cc_start: 0.8894 (ppp) cc_final: 0.8476 (tmm) REVERT: B 574 MET cc_start: 0.8578 (mmt) cc_final: 0.7959 (mmm) REVERT: B 575 TYR cc_start: 0.8489 (p90) cc_final: 0.8220 (p90) REVERT: B 672 MET cc_start: 0.9058 (tpp) cc_final: 0.8798 (tpt) REVERT: B 702 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8765 (mt-10) REVERT: B 704 GLU cc_start: 0.9274 (tp30) cc_final: 0.9047 (tm-30) REVERT: B 721 CYS cc_start: 0.8045 (p) cc_final: 0.7778 (p) REVERT: C 139 LEU cc_start: 0.9741 (mt) cc_final: 0.9510 (pp) REVERT: C 174 LYS cc_start: 0.9557 (tttp) cc_final: 0.8827 (ttpt) REVERT: C 178 ASN cc_start: 0.9328 (m110) cc_final: 0.8351 (p0) REVERT: C 214 GLU cc_start: 0.9531 (tm-30) cc_final: 0.9208 (tp30) REVERT: C 257 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8613 (mt-10) REVERT: C 261 PHE cc_start: 0.9231 (p90) cc_final: 0.8759 (p90) REVERT: C 290 THR cc_start: 0.9458 (p) cc_final: 0.9212 (t) REVERT: C 308 GLU cc_start: 0.9318 (mm-30) cc_final: 0.8745 (tt0) REVERT: C 405 GLU cc_start: 0.9607 (tt0) cc_final: 0.9191 (pt0) REVERT: C 447 PHE cc_start: 0.9183 (t80) cc_final: 0.8687 (t80) REVERT: C 448 TYR cc_start: 0.8184 (t80) cc_final: 0.7545 (t80) REVERT: C 479 MET cc_start: 0.5381 (tpt) cc_final: 0.4713 (ttt) REVERT: C 488 MET cc_start: 0.8454 (mtp) cc_final: 0.8194 (ptp) REVERT: C 508 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.5811 (tp) REVERT: C 574 MET cc_start: 0.8639 (mmt) cc_final: 0.8106 (mmm) REVERT: C 578 MET cc_start: 0.8723 (mmm) cc_final: 0.8497 (mmm) REVERT: C 598 LEU cc_start: 0.8875 (tp) cc_final: 0.8636 (tp) REVERT: C 672 MET cc_start: 0.9023 (tpp) cc_final: 0.8619 (tpt) REVERT: C 702 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8794 (mt-10) REVERT: D 139 LEU cc_start: 0.9789 (mt) cc_final: 0.9575 (pp) REVERT: D 174 LYS cc_start: 0.9530 (tttp) cc_final: 0.8711 (ttpt) REVERT: D 178 ASN cc_start: 0.9251 (m110) cc_final: 0.8282 (p0) REVERT: D 214 GLU cc_start: 0.9554 (tm-30) cc_final: 0.9200 (tp30) REVERT: D 257 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8635 (mt-10) REVERT: D 261 PHE cc_start: 0.9222 (p90) cc_final: 0.8773 (p90) REVERT: D 290 THR cc_start: 0.9408 (p) cc_final: 0.9157 (t) REVERT: D 308 GLU cc_start: 0.9331 (mm-30) cc_final: 0.8698 (tt0) REVERT: D 336 MET cc_start: 0.8637 (ttm) cc_final: 0.8437 (ttm) REVERT: D 405 GLU cc_start: 0.9611 (tt0) cc_final: 0.9213 (pt0) REVERT: D 438 LYS cc_start: 0.8987 (ptmm) cc_final: 0.8568 (tptt) REVERT: D 448 TYR cc_start: 0.8092 (t80) cc_final: 0.7609 (t80) REVERT: D 479 MET cc_start: 0.5499 (tpt) cc_final: 0.4904 (ttt) REVERT: D 488 MET cc_start: 0.8466 (mtp) cc_final: 0.8197 (ptp) REVERT: D 493 TRP cc_start: 0.8472 (t60) cc_final: 0.7765 (t60) REVERT: D 508 LEU cc_start: 0.6278 (OUTLIER) cc_final: 0.5665 (tp) REVERT: D 532 LEU cc_start: 0.9293 (mt) cc_final: 0.8909 (tp) REVERT: D 555 MET cc_start: 0.9298 (ttm) cc_final: 0.9076 (mmm) REVERT: D 574 MET cc_start: 0.8936 (mmt) cc_final: 0.8179 (mmt) REVERT: D 672 MET cc_start: 0.9061 (tpp) cc_final: 0.8830 (tpt) REVERT: D 702 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8483 (mm-30) outliers start: 91 outliers final: 47 residues processed: 490 average time/residue: 0.2494 time to fit residues: 200.3485 Evaluate side-chains 457 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 403 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 171 CYS Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 175 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 201 optimal weight: 0.0970 chunk 163 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN C 401 ASN D 401 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 20424 Z= 0.247 Angle : 0.698 13.347 27620 Z= 0.350 Chirality : 0.040 0.196 3152 Planarity : 0.003 0.026 3420 Dihedral : 5.717 38.663 2708 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.31 % Allowed : 21.34 % Favored : 74.35 % 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: 0.15 (0.17), residues: 2408 helix: 0.99 (0.13), residues: 1588 sheet: 2.17 (0.56), residues: 64 loop : -2.04 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 559 HIS 0.004 0.001 HIS C 244 PHE 0.026 0.002 PHE C 715 TYR 0.018 0.002 TYR A 575 ARG 0.003 0.000 ARG C 716 *********************** REFINEMENT MACRO_CYCLE 5 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 506 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 413 time to evaluate : 2.423 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9755 (mt) cc_final: 0.9466 (pp) REVERT: A 261 PHE cc_start: 0.9360 (p90) cc_final: 0.8807 (p90) REVERT: A 290 THR cc_start: 0.9451 (OUTLIER) cc_final: 0.9235 (t) REVERT: A 300 LEU cc_start: 0.9546 (mp) cc_final: 0.9258 (mp) REVERT: A 308 GLU cc_start: 0.9405 (mm-30) cc_final: 0.8637 (tt0) REVERT: A 448 TYR cc_start: 0.7636 (t80) cc_final: 0.7056 (t80) REVERT: A 479 MET cc_start: 0.5275 (tpt) cc_final: 0.4637 (ttt) REVERT: A 508 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6004 (tp) REVERT: A 601 PHE cc_start: 0.9208 (m-80) cc_final: 0.8928 (m-80) REVERT: A 672 MET cc_start: 0.9112 (tmm) cc_final: 0.8888 (tpt) REVERT: A 702 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8790 (mt-10) REVERT: B 174 LYS cc_start: 0.9519 (tttp) cc_final: 0.8778 (ttpt) REVERT: B 178 ASN cc_start: 0.9355 (m110) cc_final: 0.8399 (p0) REVERT: B 253 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8876 (ptmm) REVERT: B 257 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8662 (mt-10) REVERT: B 261 PHE cc_start: 0.9205 (p90) cc_final: 0.8662 (p90) REVERT: B 308 GLU cc_start: 0.9343 (mm-30) cc_final: 0.8663 (tt0) REVERT: B 405 GLU cc_start: 0.9594 (tt0) cc_final: 0.9095 (pt0) REVERT: B 448 TYR cc_start: 0.7685 (t80) cc_final: 0.7062 (t80) REVERT: B 479 MET cc_start: 0.5251 (tpt) cc_final: 0.4557 (ttt) REVERT: B 508 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6084 (tp) REVERT: B 555 MET cc_start: 0.9157 (ttm) cc_final: 0.8893 (mtp) REVERT: B 572 MET cc_start: 0.8926 (ppp) cc_final: 0.8457 (tmm) REVERT: B 575 TYR cc_start: 0.8557 (p90) cc_final: 0.8301 (p90) REVERT: B 672 MET cc_start: 0.9065 (tpp) cc_final: 0.8845 (tpt) REVERT: B 702 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8753 (mt-10) REVERT: B 721 CYS cc_start: 0.7883 (p) cc_final: 0.7569 (p) REVERT: C 174 LYS cc_start: 0.9572 (tttp) cc_final: 0.8934 (ttpt) REVERT: C 257 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8661 (mt-10) REVERT: C 261 PHE cc_start: 0.9324 (p90) cc_final: 0.8856 (p90) REVERT: C 290 THR cc_start: 0.9471 (p) cc_final: 0.9251 (t) REVERT: C 447 PHE cc_start: 0.9198 (t80) cc_final: 0.8599 (t80) REVERT: C 448 TYR cc_start: 0.8255 (t80) cc_final: 0.7637 (t80) REVERT: C 479 MET cc_start: 0.5424 (tpt) cc_final: 0.4718 (ttt) REVERT: C 488 MET cc_start: 0.8497 (mtp) cc_final: 0.8230 (ptp) REVERT: C 508 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6039 (tp) REVERT: C 555 MET cc_start: 0.9236 (tpp) cc_final: 0.8974 (mmm) REVERT: C 574 MET cc_start: 0.8930 (mmt) cc_final: 0.8337 (mmm) REVERT: C 578 MET cc_start: 0.8732 (mmm) cc_final: 0.8525 (mmm) REVERT: C 672 MET cc_start: 0.9028 (tpp) cc_final: 0.8810 (tmm) REVERT: C 702 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8886 (mt-10) REVERT: D 174 LYS cc_start: 0.9544 (tttp) cc_final: 0.8706 (ttpt) REVERT: D 178 ASN cc_start: 0.9358 (m110) cc_final: 0.8358 (p0) REVERT: D 257 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8655 (mt-10) REVERT: D 261 PHE cc_start: 0.9286 (p90) cc_final: 0.8804 (p90) REVERT: D 290 THR cc_start: 0.9461 (p) cc_final: 0.9238 (t) REVERT: D 405 GLU cc_start: 0.9627 (tt0) cc_final: 0.9236 (pt0) REVERT: D 448 TYR cc_start: 0.8225 (t80) cc_final: 0.7179 (t80) REVERT: D 479 MET cc_start: 0.5240 (tpt) cc_final: 0.4749 (ttt) REVERT: D 488 MET cc_start: 0.8493 (mtp) cc_final: 0.8199 (ptp) REVERT: D 508 LEU cc_start: 0.6392 (OUTLIER) cc_final: 0.5799 (tp) REVERT: D 532 LEU cc_start: 0.9275 (mt) cc_final: 0.8885 (tp) REVERT: D 555 MET cc_start: 0.9343 (ttm) cc_final: 0.8786 (mmm) REVERT: D 574 MET cc_start: 0.8716 (mmt) cc_final: 0.8136 (mmt) REVERT: D 672 MET cc_start: 0.9062 (tpp) cc_final: 0.8751 (tmm) REVERT: D 702 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8787 (mt-10) outliers start: 93 outliers final: 51 residues processed: 479 average time/residue: 0.2503 time to fit residues: 197.7610 Evaluate side-chains 447 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 390 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 450 PHE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 5.9990 chunk 212 optimal weight: 0.0870 chunk 46 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 236 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20424 Z= 0.185 Angle : 0.688 11.173 27620 Z= 0.335 Chirality : 0.042 0.275 3152 Planarity : 0.003 0.026 3420 Dihedral : 5.568 39.357 2708 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.80 % Allowed : 22.78 % Favored : 73.43 % 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: 0.24 (0.17), residues: 2408 helix: 1.16 (0.13), residues: 1588 sheet: 0.29 (0.78), residues: 40 loop : -2.00 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 493 HIS 0.004 0.001 HIS D 426 PHE 0.023 0.001 PHE B 445 TYR 0.025 0.002 TYR A 575 ARG 0.002 0.000 ARG C 226 *********************** REFINEMENT MACRO_CYCLE 6 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 501 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 419 time to evaluate : 2.292 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9737 (mt) cc_final: 0.9414 (pp) REVERT: A 174 LYS cc_start: 0.9566 (tttp) cc_final: 0.8875 (ttpt) REVERT: A 261 PHE cc_start: 0.9306 (p90) cc_final: 0.8715 (p90) REVERT: A 290 THR cc_start: 0.9423 (OUTLIER) cc_final: 0.9211 (t) REVERT: A 405 GLU cc_start: 0.9613 (tt0) cc_final: 0.9142 (pt0) REVERT: A 419 MET cc_start: 0.9404 (mtm) cc_final: 0.9102 (ptp) REVERT: A 448 TYR cc_start: 0.7687 (t80) cc_final: 0.7103 (t80) REVERT: A 479 MET cc_start: 0.5358 (tpt) cc_final: 0.4520 (ttt) REVERT: A 508 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.5972 (tp) REVERT: A 555 MET cc_start: 0.9287 (mmm) cc_final: 0.8896 (mmm) REVERT: A 601 PHE cc_start: 0.9210 (m-80) cc_final: 0.8672 (m-80) REVERT: A 672 MET cc_start: 0.9172 (tmm) cc_final: 0.8906 (tpt) REVERT: B 139 LEU cc_start: 0.9767 (mt) cc_final: 0.9475 (pp) REVERT: B 174 LYS cc_start: 0.9552 (tttp) cc_final: 0.8767 (ttpt) REVERT: B 177 LEU cc_start: 0.9670 (mm) cc_final: 0.9459 (mt) REVERT: B 178 ASN cc_start: 0.9305 (m110) cc_final: 0.8302 (p0) REVERT: B 253 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8837 (ptmm) REVERT: B 257 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8663 (mt-10) REVERT: B 261 PHE cc_start: 0.9171 (p90) cc_final: 0.8695 (p90) REVERT: B 290 THR cc_start: 0.9503 (p) cc_final: 0.9283 (t) REVERT: B 405 GLU cc_start: 0.9616 (tt0) cc_final: 0.9088 (pt0) REVERT: B 448 TYR cc_start: 0.7695 (t80) cc_final: 0.7088 (t80) REVERT: B 479 MET cc_start: 0.4842 (tpt) cc_final: 0.4268 (ttt) REVERT: B 488 MET cc_start: 0.8997 (ptp) cc_final: 0.8447 (ppp) REVERT: B 508 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6001 (tp) REVERT: B 555 MET cc_start: 0.9244 (ttm) cc_final: 0.8877 (mmm) REVERT: B 572 MET cc_start: 0.8951 (ppp) cc_final: 0.8458 (tmm) REVERT: B 575 TYR cc_start: 0.8477 (p90) cc_final: 0.8180 (p90) REVERT: B 672 MET cc_start: 0.9068 (tpp) cc_final: 0.8853 (tpt) REVERT: B 721 CYS cc_start: 0.7983 (p) cc_final: 0.7594 (p) REVERT: C 139 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9442 (pp) REVERT: C 174 LYS cc_start: 0.9572 (tttp) cc_final: 0.9020 (ttpt) REVERT: C 257 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8652 (mt-10) REVERT: C 261 PHE cc_start: 0.9283 (p90) cc_final: 0.8833 (p90) REVERT: C 290 THR cc_start: 0.9421 (p) cc_final: 0.9208 (t) REVERT: C 405 GLU cc_start: 0.9611 (tt0) cc_final: 0.9126 (pt0) REVERT: C 447 PHE cc_start: 0.9226 (t80) cc_final: 0.8613 (t80) REVERT: C 448 TYR cc_start: 0.8330 (t80) cc_final: 0.7702 (t80) REVERT: C 479 MET cc_start: 0.5325 (tpt) cc_final: 0.4664 (ttt) REVERT: C 488 MET cc_start: 0.8557 (mtp) cc_final: 0.8238 (ptp) REVERT: C 508 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.5963 (tp) REVERT: C 555 MET cc_start: 0.9267 (tpp) cc_final: 0.9010 (mmm) REVERT: C 574 MET cc_start: 0.8923 (mmt) cc_final: 0.8371 (mmm) REVERT: C 601 PHE cc_start: 0.9217 (m-80) cc_final: 0.8824 (m-80) REVERT: C 661 TYR cc_start: 0.7094 (t80) cc_final: 0.6064 (t80) REVERT: C 672 MET cc_start: 0.9031 (tpp) cc_final: 0.8782 (tmm) REVERT: D 139 LEU cc_start: 0.9734 (OUTLIER) cc_final: 0.9521 (pp) REVERT: D 174 LYS cc_start: 0.9540 (tttp) cc_final: 0.8748 (ttpt) REVERT: D 178 ASN cc_start: 0.9350 (m110) cc_final: 0.8367 (p0) REVERT: D 257 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8667 (mt-10) REVERT: D 261 PHE cc_start: 0.9241 (p90) cc_final: 0.8751 (p90) REVERT: D 290 THR cc_start: 0.9456 (p) cc_final: 0.9233 (t) REVERT: D 405 GLU cc_start: 0.9617 (tt0) cc_final: 0.9139 (pt0) REVERT: D 479 MET cc_start: 0.4963 (tpt) cc_final: 0.4467 (ttt) REVERT: D 493 TRP cc_start: 0.9062 (t-100) cc_final: 0.8336 (t60) REVERT: D 508 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.5842 (tp) REVERT: D 532 LEU cc_start: 0.9239 (mt) cc_final: 0.8830 (tp) REVERT: D 574 MET cc_start: 0.8639 (mmt) cc_final: 0.8212 (mmt) REVERT: D 601 PHE cc_start: 0.9194 (m-80) cc_final: 0.8734 (m-80) REVERT: D 672 MET cc_start: 0.9086 (tpp) cc_final: 0.8713 (tmm) REVERT: D 676 LEU cc_start: 0.9557 (pp) cc_final: 0.9094 (pp) outliers start: 82 outliers final: 54 residues processed: 472 average time/residue: 0.2681 time to fit residues: 211.8623 Evaluate side-chains 454 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 392 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.3865 > 50: distance: 51 - 69: 26.893 distance: 55 - 80: 26.378 distance: 60 - 87: 28.657 distance: 64 - 69: 29.301 distance: 65 - 95: 34.657 distance: 69 - 70: 13.869 distance: 70 - 71: 54.957 distance: 70 - 73: 16.137 distance: 71 - 72: 44.885 distance: 71 - 80: 16.848 distance: 73 - 74: 58.488 distance: 74 - 75: 29.624 distance: 74 - 76: 24.173 distance: 75 - 77: 57.543 distance: 76 - 78: 47.949 distance: 77 - 79: 33.916 distance: 78 - 79: 10.511 distance: 80 - 81: 41.894 distance: 81 - 82: 9.823 distance: 81 - 84: 16.571 distance: 82 - 83: 30.252 distance: 82 - 87: 8.322 distance: 83 - 111: 35.303 distance: 84 - 85: 31.767 distance: 84 - 86: 30.661 distance: 87 - 88: 39.883 distance: 88 - 89: 18.300 distance: 88 - 91: 24.296 distance: 89 - 90: 21.281 distance: 89 - 95: 51.841 distance: 90 - 119: 41.882 distance: 91 - 92: 54.941 distance: 92 - 93: 44.318 distance: 92 - 94: 42.855 distance: 95 - 96: 5.370 distance: 96 - 97: 39.723 distance: 96 - 99: 39.463 distance: 97 - 98: 37.100 distance: 97 - 103: 54.093 distance: 98 - 127: 12.223 distance: 99 - 100: 43.997 distance: 100 - 101: 38.519 distance: 100 - 102: 27.630 distance: 103 - 104: 36.467 distance: 104 - 105: 36.395 distance: 104 - 107: 51.387 distance: 105 - 106: 54.800 distance: 105 - 111: 41.145 distance: 106 - 135: 53.303 distance: 107 - 108: 47.226 distance: 108 - 109: 56.024 distance: 108 - 110: 3.490 distance: 111 - 112: 30.287 distance: 112 - 113: 40.603 distance: 112 - 115: 46.277 distance: 113 - 114: 19.657 distance: 113 - 119: 21.233 distance: 114 - 143: 24.435 distance: 115 - 116: 26.362 distance: 116 - 117: 29.714 distance: 116 - 118: 24.493 distance: 119 - 120: 17.598 distance: 120 - 121: 8.521 distance: 120 - 123: 5.911 distance: 121 - 122: 32.360 distance: 121 - 127: 42.641 distance: 122 - 148: 19.586 distance: 123 - 124: 25.082 distance: 124 - 125: 22.149 distance: 125 - 126: 31.533 distance: 127 - 128: 27.785 distance: 128 - 129: 20.598 distance: 128 - 131: 23.823 distance: 129 - 135: 40.840 distance: 131 - 132: 16.618 distance: 132 - 133: 35.751 distance: 132 - 134: 26.668 distance: 135 - 136: 27.734 distance: 136 - 137: 10.991 distance: 136 - 139: 25.176 distance: 137 - 138: 29.626 distance: 137 - 143: 11.581 distance: 138 - 163: 28.650 distance: 139 - 140: 36.131 distance: 139 - 141: 30.542 distance: 140 - 142: 9.439 distance: 143 - 144: 11.746 distance: 144 - 145: 5.355 distance: 144 - 147: 8.700 distance: 145 - 146: 7.123 distance: 145 - 148: 10.534 distance: 146 - 167: 17.025