Starting phenix.real_space_refine on Mon Dec 11 08:14:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkg_40183/12_2023/8gkg_40183.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkg_40183/12_2023/8gkg_40183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkg_40183/12_2023/8gkg_40183.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkg_40183/12_2023/8gkg_40183.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkg_40183/12_2023/8gkg_40183.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkg_40183/12_2023/8gkg_40183.pdb" } resolution = 4.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 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 50 5.16 5 C 10755 2.51 5 N 3095 2.21 5 O 3260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 719": "OE1" <-> "OE2" Residue "B PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 719": "OE1" <-> "OE2" Residue "C PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 719": "OE1" <-> "OE2" Residue "D PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 719": "OE1" <-> "OE2" Residue "E PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 719": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 17160 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 3432 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 269} Link IDs: {'PTRANS': 12, 'TRANS': 527} Chain breaks: 4 Unresolved non-hydrogen bonds: 985 Unresolved non-hydrogen angles: 1258 Unresolved non-hydrogen dihedrals: 798 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 12, 'TRP:plan': 3, 'ASP:plan': 12, 'PHE:plan': 16, 'GLU:plan': 25, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 500 Chain: "B" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 3432 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 269} Link IDs: {'PTRANS': 12, 'TRANS': 527} Chain breaks: 4 Unresolved non-hydrogen bonds: 985 Unresolved non-hydrogen angles: 1258 Unresolved non-hydrogen dihedrals: 798 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 12, 'TRP:plan': 3, 'ASP:plan': 12, 'PHE:plan': 16, 'GLU:plan': 25, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 500 Chain: "C" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 3432 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 269} Link IDs: {'PTRANS': 12, 'TRANS': 527} Chain breaks: 4 Unresolved non-hydrogen bonds: 985 Unresolved non-hydrogen angles: 1258 Unresolved non-hydrogen dihedrals: 798 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 12, 'TRP:plan': 3, 'ASP:plan': 12, 'PHE:plan': 16, 'GLU:plan': 25, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 500 Chain: "D" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 3432 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 269} Link IDs: {'PTRANS': 12, 'TRANS': 527} Chain breaks: 4 Unresolved non-hydrogen bonds: 985 Unresolved non-hydrogen angles: 1258 Unresolved non-hydrogen dihedrals: 798 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 12, 'TRP:plan': 3, 'ASP:plan': 12, 'PHE:plan': 16, 'GLU:plan': 25, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 500 Chain: "E" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 3432 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 269} Link IDs: {'PTRANS': 12, 'TRANS': 527} Chain breaks: 4 Unresolved non-hydrogen bonds: 985 Unresolved non-hydrogen angles: 1258 Unresolved non-hydrogen dihedrals: 798 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 12, 'TRP:plan': 3, 'ASP:plan': 12, 'PHE:plan': 16, 'GLU:plan': 25, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 500 Time building chain proxies: 9.93, per 1000 atoms: 0.58 Number of scatterers: 17160 At special positions: 0 Unit cell: (170.008, 172.16, 110.828, 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 50 16.00 O 3260 8.00 N 3095 7.00 C 10755 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: 7.19 Conformation dependent library (CDL) restraints added in 3.7 seconds 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5160 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 0 sheets defined 61.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 132 through 148 Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 180 through 196 removed outlier: 4.358A pdb=" N GLU A 185 " --> pdb=" O PRO A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 216 through 225 removed outlier: 3.501A pdb=" N ASN A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 239 through 243 removed outlier: 3.639A pdb=" N ASN A 242 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 298 through 306 removed outlier: 4.216A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 328 removed outlier: 4.011A pdb=" N MET A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 removed outlier: 3.950A pdb=" N LEU A 333 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.351A pdb=" N GLY A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.570A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.699A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 432 through 440 removed outlier: 3.649A pdb=" N ALA A 437 " --> pdb=" O TRP A 433 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 447 removed outlier: 3.555A pdb=" N PHE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 461 Processing helix chain 'A' and resid 487 through 505 removed outlier: 3.627A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 535 removed outlier: 3.814A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL A 531 " --> pdb=" O PHE A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 568 removed outlier: 4.250A pdb=" N MET A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 605 Processing helix chain 'A' and resid 629 through 634 removed outlier: 3.547A pdb=" N LEU A 632 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 634 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 679 removed outlier: 3.798A pdb=" N LEU A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 685 removed outlier: 3.886A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 702 removed outlier: 4.337A pdb=" N ARG A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 707 removed outlier: 3.893A pdb=" N LEU A 707 " --> pdb=" O GLU A 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 130 Processing helix chain 'B' and resid 132 through 148 Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.357A pdb=" N GLU B 185 " --> pdb=" O PRO B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 216 through 225 removed outlier: 3.501A pdb=" N ASN B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.640A pdb=" N ASN B 242 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 298 through 306 removed outlier: 4.217A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR B 305 " --> pdb=" O HIS B 301 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 328 removed outlier: 4.011A pdb=" N MET B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR B 321 " --> pdb=" O VAL B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.950A pdb=" N LEU B 333 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 removed outlier: 4.352A pdb=" N GLY B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 removed outlier: 3.570A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.699A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 432 through 440 removed outlier: 3.648A pdb=" N ALA B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LYS B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 447 removed outlier: 3.555A pdb=" N PHE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS B 446 " --> pdb=" O PHE B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 461 Processing helix chain 'B' and resid 487 through 505 removed outlier: 3.628A pdb=" N ILE B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 535 removed outlier: 3.814A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL B 531 " --> pdb=" O PHE B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 568 removed outlier: 4.250A pdb=" N MET B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 605 Processing helix chain 'B' and resid 629 through 634 removed outlier: 3.547A pdb=" N LEU B 632 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 634 " --> pdb=" O GLU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 679 removed outlier: 3.797A pdb=" N LEU B 657 " --> pdb=" O LEU B 653 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 685 removed outlier: 3.886A pdb=" N ASN B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 702 removed outlier: 4.337A pdb=" N ARG B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 707 removed outlier: 3.893A pdb=" N LEU B 707 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 132 through 148 Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 180 through 196 removed outlier: 4.357A pdb=" N GLU C 185 " --> pdb=" O PRO C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.502A pdb=" N ASN C 220 " --> pdb=" O GLN C 216 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.640A pdb=" N ASN C 242 " --> pdb=" O ALA C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 298 through 306 removed outlier: 4.216A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR C 305 " --> pdb=" O HIS C 301 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 328 removed outlier: 4.011A pdb=" N MET C 320 " --> pdb=" O PHE C 316 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR C 321 " --> pdb=" O VAL C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 335 removed outlier: 3.949A pdb=" N LEU C 333 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 removed outlier: 4.351A pdb=" N GLY C 341 " --> pdb=" O ARG C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.571A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET C 351 " --> pdb=" O LEU C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.698A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 432 through 440 removed outlier: 3.649A pdb=" N ALA C 437 " --> pdb=" O TRP C 433 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS C 438 " --> pdb=" O LYS C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 447 removed outlier: 3.555A pdb=" N PHE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS C 446 " --> pdb=" O PHE C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 461 Processing helix chain 'C' and resid 487 through 505 removed outlier: 3.628A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 535 removed outlier: 3.815A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL C 531 " --> pdb=" O PHE C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 568 removed outlier: 4.250A pdb=" N MET C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 605 Processing helix chain 'C' and resid 629 through 634 removed outlier: 3.548A pdb=" N LEU C 632 " --> pdb=" O VAL C 629 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS C 634 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 679 removed outlier: 3.797A pdb=" N LEU C 657 " --> pdb=" O LEU C 653 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 685 removed outlier: 3.886A pdb=" N ASN C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 702 removed outlier: 4.337A pdb=" N ARG C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 707 removed outlier: 3.893A pdb=" N LEU C 707 " --> pdb=" O GLU C 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 130 Processing helix chain 'D' and resid 132 through 148 Processing helix chain 'D' and resid 172 through 178 Processing helix chain 'D' and resid 180 through 196 removed outlier: 4.357A pdb=" N GLU D 185 " --> pdb=" O PRO D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 216 through 225 removed outlier: 3.501A pdb=" N ASN D 220 " --> pdb=" O GLN D 216 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG D 225 " --> pdb=" O ILE D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 239 through 243 removed outlier: 3.640A pdb=" N ASN D 242 " --> pdb=" O ALA D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 298 through 306 removed outlier: 4.216A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR D 305 " --> pdb=" O HIS D 301 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 328 removed outlier: 4.011A pdb=" N MET D 320 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR D 321 " --> pdb=" O VAL D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 335 removed outlier: 3.949A pdb=" N LEU D 333 " --> pdb=" O ASN D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 342 removed outlier: 4.352A pdb=" N GLY D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 removed outlier: 3.570A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.699A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 432 through 440 removed outlier: 3.648A pdb=" N ALA D 437 " --> pdb=" O TRP D 433 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS D 438 " --> pdb=" O LYS D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 447 removed outlier: 3.554A pdb=" N PHE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS D 446 " --> pdb=" O PHE D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 461 Processing helix chain 'D' and resid 487 through 505 removed outlier: 3.628A pdb=" N ILE D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 535 removed outlier: 3.814A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL D 531 " --> pdb=" O PHE D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 568 removed outlier: 4.250A pdb=" N MET D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 605 Processing helix chain 'D' and resid 629 through 634 removed outlier: 3.547A pdb=" N LEU D 632 " --> pdb=" O VAL D 629 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS D 634 " --> pdb=" O GLU D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 679 removed outlier: 3.798A pdb=" N LEU D 657 " --> pdb=" O LEU D 653 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 685 removed outlier: 3.886A pdb=" N ASN D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 702 removed outlier: 4.338A pdb=" N ARG D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 707 removed outlier: 3.894A pdb=" N LEU D 707 " --> pdb=" O GLU D 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 130 Processing helix chain 'E' and resid 132 through 148 Processing helix chain 'E' and resid 172 through 178 Processing helix chain 'E' and resid 180 through 196 removed outlier: 4.357A pdb=" N GLU E 185 " --> pdb=" O PRO E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 205 Processing helix chain 'E' and resid 216 through 225 removed outlier: 3.502A pdb=" N ASN E 220 " --> pdb=" O GLN E 216 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE E 221 " --> pdb=" O THR E 217 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG E 225 " --> pdb=" O ILE E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 238 Processing helix chain 'E' and resid 239 through 243 removed outlier: 3.639A pdb=" N ASN E 242 " --> pdb=" O ALA E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 272 Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 298 through 306 removed outlier: 4.216A pdb=" N VAL E 304 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR E 305 " --> pdb=" O HIS E 301 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL E 306 " --> pdb=" O ALA E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 328 removed outlier: 4.011A pdb=" N MET E 320 " --> pdb=" O PHE E 316 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR E 321 " --> pdb=" O VAL E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 335 removed outlier: 3.949A pdb=" N LEU E 333 " --> pdb=" O ASN E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 342 removed outlier: 4.352A pdb=" N GLY E 341 " --> pdb=" O ARG E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 351 removed outlier: 3.570A pdb=" N ALA E 349 " --> pdb=" O LEU E 345 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET E 351 " --> pdb=" O LEU E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 362 removed outlier: 3.698A pdb=" N TYR E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 421 Processing helix chain 'E' and resid 432 through 440 removed outlier: 3.648A pdb=" N ALA E 437 " --> pdb=" O TRP E 433 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LYS E 438 " --> pdb=" O LYS E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 447 removed outlier: 3.554A pdb=" N PHE E 445 " --> pdb=" O PHE E 441 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS E 446 " --> pdb=" O PHE E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 461 Processing helix chain 'E' and resid 487 through 505 removed outlier: 3.628A pdb=" N ILE E 492 " --> pdb=" O MET E 488 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP E 493 " --> pdb=" O PHE E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 535 removed outlier: 3.815A pdb=" N VAL E 525 " --> pdb=" O TRP E 521 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL E 531 " --> pdb=" O PHE E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 568 removed outlier: 4.249A pdb=" N MET E 555 " --> pdb=" O LEU E 551 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 563 " --> pdb=" O TRP E 559 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR E 565 " --> pdb=" O ASN E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 605 Processing helix chain 'E' and resid 629 through 634 removed outlier: 3.547A pdb=" N LEU E 632 " --> pdb=" O VAL E 629 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS E 634 " --> pdb=" O GLU E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 653 through 679 removed outlier: 3.798A pdb=" N LEU E 657 " --> pdb=" O LEU E 653 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE E 659 " --> pdb=" O LEU E 655 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU E 679 " --> pdb=" O ALA E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 685 removed outlier: 3.886A pdb=" N ASN E 683 " --> pdb=" O GLU E 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 688 through 702 removed outlier: 4.337A pdb=" N ARG E 693 " --> pdb=" O GLU E 689 " (cutoff:3.500A) Processing helix chain 'E' and resid 703 through 707 removed outlier: 3.894A pdb=" N LEU E 707 " --> pdb=" O GLU E 704 " (cutoff:3.500A) 921 hydrogen bonds defined for protein. 2688 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.53 Time building geometry restraints manager: 7.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6060 1.34 - 1.46: 3001 1.46 - 1.57: 8264 1.57 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 17420 Sorted by residual: bond pdb=" C VAL E 154 " pdb=" N PRO E 155 " ideal model delta sigma weight residual 1.339 1.378 -0.039 3.40e-02 8.65e+02 1.34e+00 bond pdb=" C VAL B 154 " pdb=" N PRO B 155 " ideal model delta sigma weight residual 1.339 1.378 -0.039 3.40e-02 8.65e+02 1.32e+00 bond pdb=" C VAL D 154 " pdb=" N PRO D 155 " ideal model delta sigma weight residual 1.339 1.378 -0.039 3.40e-02 8.65e+02 1.32e+00 bond pdb=" C VAL C 154 " pdb=" N PRO C 155 " ideal model delta sigma weight residual 1.339 1.378 -0.039 3.40e-02 8.65e+02 1.30e+00 bond pdb=" C VAL A 154 " pdb=" N PRO A 155 " ideal model delta sigma weight residual 1.339 1.378 -0.038 3.40e-02 8.65e+02 1.27e+00 ... (remaining 17415 not shown) Histogram of bond angle deviations from ideal: 100.50 - 107.20: 401 107.20 - 113.90: 9695 113.90 - 120.60: 7160 120.60 - 127.30: 6534 127.30 - 134.00: 125 Bond angle restraints: 23915 Sorted by residual: angle pdb=" N ARG C 716 " pdb=" CA ARG C 716 " pdb=" C ARG C 716 " ideal model delta sigma weight residual 107.73 111.83 -4.10 1.34e+00 5.57e-01 9.36e+00 angle pdb=" N ARG E 716 " pdb=" CA ARG E 716 " pdb=" C ARG E 716 " ideal model delta sigma weight residual 107.73 111.83 -4.10 1.34e+00 5.57e-01 9.35e+00 angle pdb=" N ARG D 716 " pdb=" CA ARG D 716 " pdb=" C ARG D 716 " ideal model delta sigma weight residual 107.73 111.82 -4.09 1.34e+00 5.57e-01 9.30e+00 angle pdb=" N ARG A 716 " pdb=" CA ARG A 716 " pdb=" C ARG A 716 " ideal model delta sigma weight residual 107.73 111.81 -4.08 1.34e+00 5.57e-01 9.25e+00 angle pdb=" N ARG B 716 " pdb=" CA ARG B 716 " pdb=" C ARG B 716 " ideal model delta sigma weight residual 107.73 111.77 -4.04 1.34e+00 5.57e-01 9.09e+00 ... (remaining 23910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.17: 9219 12.17 - 24.34: 556 24.34 - 36.50: 345 36.50 - 48.67: 60 48.67 - 60.84: 35 Dihedral angle restraints: 10215 sinusoidal: 2325 harmonic: 7890 Sorted by residual: dihedral pdb=" CA TYR E 254 " pdb=" C TYR E 254 " pdb=" N GLN E 255 " pdb=" CA GLN E 255 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA TYR C 254 " pdb=" C TYR C 254 " pdb=" N GLN C 255 " pdb=" CA GLN C 255 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA TYR D 254 " pdb=" C TYR D 254 " pdb=" N GLN D 255 " pdb=" CA GLN D 255 " ideal model delta harmonic sigma weight residual 180.00 -160.49 -19.51 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 10212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1807 0.035 - 0.070: 926 0.070 - 0.104: 150 0.104 - 0.139: 17 0.139 - 0.174: 5 Chirality restraints: 2905 Sorted by residual: chirality pdb=" CB ILE A 644 " pdb=" CA ILE A 644 " pdb=" CG1 ILE A 644 " pdb=" CG2 ILE A 644 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CB ILE E 644 " pdb=" CA ILE E 644 " pdb=" CG1 ILE E 644 " pdb=" CG2 ILE E 644 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CB ILE B 644 " pdb=" CA ILE B 644 " pdb=" CG1 ILE B 644 " pdb=" CG2 ILE B 644 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.41e-01 ... (remaining 2902 not shown) Planarity restraints: 3225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 274 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO C 275 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 275 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 275 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 274 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO A 275 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 275 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 275 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 274 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO E 275 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO E 275 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 275 " -0.024 5.00e-02 4.00e+02 ... (remaining 3222 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5489 2.81 - 3.34: 17749 3.34 - 3.86: 25065 3.86 - 4.38: 27052 4.38 - 4.90: 42459 Nonbonded interactions: 117814 Sorted by model distance: nonbonded pdb=" NH1 ARG E 712 " pdb=" O SER E 713 " model vdw 2.293 2.520 nonbonded pdb=" NH1 ARG B 712 " pdb=" O SER B 713 " model vdw 2.294 2.520 nonbonded pdb=" NH1 ARG C 712 " pdb=" O SER C 713 " model vdw 2.294 2.520 nonbonded pdb=" NH1 ARG A 712 " pdb=" O SER A 713 " model vdw 2.294 2.520 nonbonded pdb=" NH1 ARG D 712 " pdb=" O SER D 713 " model vdw 2.294 2.520 ... (remaining 117809 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' selection = chain 'E' } 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.700 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 46.380 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17420 Z= 0.157 Angle : 0.542 5.386 23915 Z= 0.293 Chirality : 0.038 0.174 2905 Planarity : 0.003 0.043 3225 Dihedral : 12.426 60.840 5055 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.30 % Favored : 83.51 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.17), residues: 2650 helix: 0.09 (0.15), residues: 1345 sheet: None (None), residues: 0 loop : -3.02 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 692 HIS 0.001 0.000 HIS E 585 PHE 0.017 0.001 PHE C 445 TYR 0.014 0.001 TYR D 594 ARG 0.003 0.000 ARG C 712 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2601 time to fit residues: 121.8491 Evaluate side-chains 258 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 1.780 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 9.9990 chunk 204 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 138 optimal weight: 0.0770 chunk 109 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 128 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 overall best weight: 3.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17420 Z= 0.282 Angle : 0.663 7.545 23915 Z= 0.372 Chirality : 0.042 0.141 2905 Planarity : 0.005 0.042 3225 Dihedral : 4.771 21.448 2780 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.64 % Favored : 83.17 % Rotamer: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.16), residues: 2650 helix: -0.15 (0.13), residues: 1430 sheet: None (None), residues: 0 loop : -3.80 (0.15), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 692 HIS 0.004 0.001 HIS A 426 PHE 0.019 0.002 PHE A 449 TYR 0.034 0.003 TYR A 594 ARG 0.006 0.001 ARG D 690 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.2712 time to fit residues: 120.9037 Evaluate side-chains 257 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.940 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 265 optimal weight: 9.9990 chunk 218 optimal weight: 30.0000 chunk 243 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17420 Z= 0.187 Angle : 0.595 9.350 23915 Z= 0.322 Chirality : 0.041 0.158 2905 Planarity : 0.004 0.044 3225 Dihedral : 4.472 20.711 2780 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.11 % Favored : 83.70 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.16), residues: 2650 helix: 0.35 (0.14), residues: 1410 sheet: None (None), residues: 0 loop : -3.71 (0.16), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 692 HIS 0.002 0.001 HIS C 585 PHE 0.023 0.002 PHE B 597 TYR 0.037 0.002 TYR A 594 ARG 0.008 0.000 ARG B 712 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.2806 time to fit residues: 128.4133 Evaluate side-chains 262 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.897 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 0.0770 chunk 184 optimal weight: 0.8980 chunk 127 optimal weight: 0.0670 chunk 27 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 164 optimal weight: 8.9990 chunk 246 optimal weight: 8.9990 chunk 260 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17420 Z= 0.157 Angle : 0.554 6.070 23915 Z= 0.298 Chirality : 0.040 0.132 2905 Planarity : 0.003 0.042 3225 Dihedral : 4.234 20.786 2780 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.62 % Favored : 84.19 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.17), residues: 2650 helix: 0.67 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -3.65 (0.16), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 692 HIS 0.003 0.001 HIS B 439 PHE 0.015 0.001 PHE C 449 TYR 0.035 0.002 TYR A 594 ARG 0.004 0.000 ARG A 690 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.2832 time to fit residues: 127.1837 Evaluate side-chains 266 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.880 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 5.9990 chunk 148 optimal weight: 0.6980 chunk 3 optimal weight: 50.0000 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 222 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 133 optimal weight: 9.9990 chunk 234 optimal weight: 0.4980 chunk 65 optimal weight: 9.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17420 Z= 0.273 Angle : 0.678 7.056 23915 Z= 0.374 Chirality : 0.043 0.192 2905 Planarity : 0.005 0.055 3225 Dihedral : 5.035 25.083 2780 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.23 % Allowed : 17.77 % Favored : 82.00 % Rotamer: Outliers : 0.10 % Allowed : 5.27 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.16), residues: 2650 helix: 0.27 (0.14), residues: 1410 sheet: None (None), residues: 0 loop : -3.89 (0.16), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 692 HIS 0.005 0.001 HIS C 585 PHE 0.021 0.002 PHE A 449 TYR 0.034 0.003 TYR A 594 ARG 0.006 0.001 ARG D 690 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 307 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 308 average time/residue: 0.2741 time to fit residues: 129.2628 Evaluate side-chains 268 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 267 time to evaluate : 1.885 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1537 time to fit residues: 2.9277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 3.9990 chunk 235 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 153 optimal weight: 0.2980 chunk 64 optimal weight: 0.0470 chunk 261 optimal weight: 4.9990 chunk 216 optimal weight: 30.0000 chunk 120 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 overall best weight: 1.6684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17420 Z= 0.180 Angle : 0.607 6.819 23915 Z= 0.327 Chirality : 0.041 0.140 2905 Planarity : 0.004 0.050 3225 Dihedral : 4.674 22.683 2780 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.89 % Favored : 83.92 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.16), residues: 2650 helix: 0.57 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -3.84 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 692 HIS 0.002 0.001 HIS C 585 PHE 0.022 0.002 PHE A 449 TYR 0.037 0.002 TYR A 594 ARG 0.006 0.001 ARG D 690 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 1.975 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.3145 time to fit residues: 143.5709 Evaluate side-chains 264 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.884 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 chunk 190 optimal weight: 10.0000 chunk 147 optimal weight: 0.8980 chunk 219 optimal weight: 0.0010 chunk 145 optimal weight: 1.9990 chunk 260 optimal weight: 6.9990 chunk 162 optimal weight: 30.0000 chunk 158 optimal weight: 9.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17420 Z= 0.158 Angle : 0.579 6.999 23915 Z= 0.309 Chirality : 0.040 0.134 2905 Planarity : 0.004 0.044 3225 Dihedral : 4.326 21.039 2780 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.11 % Favored : 83.70 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.17), residues: 2650 helix: 0.89 (0.14), residues: 1430 sheet: None (None), residues: 0 loop : -3.72 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 692 HIS 0.003 0.001 HIS C 439 PHE 0.020 0.001 PHE D 445 TYR 0.038 0.002 TYR A 594 ARG 0.008 0.001 ARG D 690 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.2792 time to fit residues: 129.8345 Evaluate side-chains 261 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 2.010 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 165 optimal weight: 0.1980 chunk 177 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 204 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17420 Z= 0.152 Angle : 0.570 6.919 23915 Z= 0.301 Chirality : 0.040 0.187 2905 Planarity : 0.003 0.039 3225 Dihedral : 4.203 20.857 2780 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.25 % Favored : 84.57 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.17), residues: 2650 helix: 1.02 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -3.68 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 692 HIS 0.002 0.001 HIS A 585 PHE 0.020 0.001 PHE E 449 TYR 0.036 0.002 TYR A 594 ARG 0.005 0.000 ARG C 690 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 1.879 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2811 time to fit residues: 130.1246 Evaluate side-chains 259 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 1.736 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 0.9990 chunk 249 optimal weight: 0.7980 chunk 227 optimal weight: 0.9980 chunk 242 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 190 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 219 optimal weight: 40.0000 chunk 229 optimal weight: 3.9990 chunk 241 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17420 Z= 0.150 Angle : 0.569 6.778 23915 Z= 0.298 Chirality : 0.040 0.292 2905 Planarity : 0.003 0.038 3225 Dihedral : 4.087 20.859 2780 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.25 % Favored : 84.57 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.17), residues: 2650 helix: 1.07 (0.14), residues: 1465 sheet: None (None), residues: 0 loop : -3.75 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 692 HIS 0.002 0.000 HIS A 585 PHE 0.019 0.001 PHE A 124 TYR 0.041 0.001 TYR E 594 ARG 0.005 0.000 ARG D 690 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 1.809 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.2786 time to fit residues: 128.5119 Evaluate side-chains 261 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.817 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 10.0000 chunk 256 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 chunk 247 optimal weight: 0.3980 chunk 214 optimal weight: 8.9990 chunk 22 optimal weight: 0.0970 chunk 165 optimal weight: 20.0000 chunk 131 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17420 Z= 0.157 Angle : 0.578 6.737 23915 Z= 0.304 Chirality : 0.041 0.293 2905 Planarity : 0.003 0.037 3225 Dihedral : 4.111 20.705 2780 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.74 % Favored : 84.08 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2650 helix: 1.08 (0.14), residues: 1465 sheet: None (None), residues: 0 loop : -3.73 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 692 HIS 0.002 0.001 HIS A 585 PHE 0.019 0.001 PHE B 449 TYR 0.041 0.002 TYR D 594 ARG 0.005 0.001 ARG C 712 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 1.837 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.2786 time to fit residues: 131.4606 Evaluate side-chains 261 residues out of total 2375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 2.002 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.2339 > 50: distance: 36 - 41: 28.700 distance: 41 - 42: 31.233 distance: 42 - 43: 19.980 distance: 42 - 45: 21.883 distance: 43 - 44: 34.012 distance: 43 - 46: 56.076 distance: 46 - 47: 39.986 distance: 47 - 48: 37.562 distance: 47 - 50: 39.613 distance: 48 - 49: 38.314 distance: 48 - 54: 3.822 distance: 50 - 51: 39.863 distance: 54 - 55: 57.241 distance: 55 - 56: 39.459 distance: 56 - 59: 6.958 distance: 59 - 60: 51.857 distance: 60 - 63: 39.250 distance: 61 - 62: 40.163 distance: 65 - 68: 40.443 distance: 66 - 67: 28.472 distance: 66 - 73: 33.382 distance: 67 - 92: 49.452 distance: 69 - 70: 46.007 distance: 70 - 71: 18.099 distance: 73 - 74: 39.844 distance: 75 - 78: 40.468 distance: 79 - 82: 39.803 distance: 80 - 81: 56.301 distance: 83 - 84: 40.219 distance: 84 - 85: 42.769 distance: 84 - 87: 41.476 distance: 85 - 86: 17.274 distance: 85 - 92: 23.762 distance: 86 - 113: 33.058 distance: 87 - 88: 41.184 distance: 90 - 91: 40.419 distance: 95 - 123: 37.137 distance: 104 - 105: 57.317 distance: 105 - 106: 41.000 distance: 105 - 108: 33.717