Starting phenix.real_space_refine on Thu Jun 12 19:57:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6itc_9731/06_2025/6itc_9731.cif Found real_map, /net/cci-nas-00/data/ceres_data/6itc_9731/06_2025/6itc_9731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6itc_9731/06_2025/6itc_9731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6itc_9731/06_2025/6itc_9731.map" model { file = "/net/cci-nas-00/data/ceres_data/6itc_9731/06_2025/6itc_9731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6itc_9731/06_2025/6itc_9731.cif" } resolution = 3.45 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= 0.004 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: 8 Type Number sf(0) Gaussians P 4 5.49 5 Mg 1 5.21 5 S 64 5.16 5 Be 1 3.05 5 C 8811 2.51 5 N 2365 2.21 5 O 2595 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13844 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 6107 Classifications: {'peptide': 765} Link IDs: {'PTRANS': 15, 'TRANS': 749} Chain: "Y" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3275 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 1 Chain: "E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 480 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "V" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 110} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 312 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain breaks: 1 Chain: "G" Number of atoms: 469 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 62, 466 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Conformer: "B" Number of residues, atoms: 62, 466 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} bond proxies already assigned to first conformer: 473 Chain: "G" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1333 Unusual residues: {'GYS': 1} Classifications: {'peptide': 162, 'undetermined': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 155, None: 1} Not linked: pdbres="GYS G 66 " pdbres="VAL G 68 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GYS:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 868 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'PGV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1, 'PGV:plan-1': 1} Unresolved non-hydrogen planarities: 8 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N SER V 25 " occ=0.09 ... (4 atoms not shown) pdb=" OG SER V 25 " occ=0.09 residue: pdb=" N LYS V 86 " occ=0.84 ... (3 atoms not shown) pdb=" CB LYS V 86 " occ=0.84 residue: pdb=" N CYS V 95 " occ=0.93 ... (4 atoms not shown) pdb=" SG CYS V 95 " occ=0.93 Time building chain proxies: 8.93, per 1000 atoms: 0.65 Number of scatterers: 13844 At special positions: 0 Unit cell: (128.1, 99.75, 155.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 64 16.00 P 4 15.00 Mg 1 11.99 F 3 9.00 O 2595 8.00 N 2365 7.00 C 8811 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS Y 60 " - pdb=" SG CYS B 29 " distance=2.06 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 95 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of additional links: simple=1, symmetry=0 Simple link: pdb=" C PHE G 64 " - pdb=" N GYS G 66 " Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.97 Conformation dependent library (CDL) restraints added in 1.8 seconds 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3206 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 16 sheets defined 48.6% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 14 through 30 removed outlier: 3.606A pdb=" N ARG A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 30 " --> pdb=" O ILE A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 40 through 53 Processing helix chain 'A' and resid 61 through 78 removed outlier: 3.650A pdb=" N ALA A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 106 through 118 removed outlier: 3.658A pdb=" N THR A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 130 through 147 removed outlier: 4.921A pdb=" N LYS A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 177 through 188 Processing helix chain 'A' and resid 192 through 196 removed outlier: 3.560A pdb=" N GLN A 195 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET A 196 " --> pdb=" O LYS A 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 192 through 196' Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 231 through 242 removed outlier: 3.628A pdb=" N VAL A 235 " --> pdb=" O THR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 249 removed outlier: 3.570A pdb=" N ASP A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 245 through 249' Processing helix chain 'A' and resid 262 through 273 removed outlier: 3.694A pdb=" N THR A 267 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 299 removed outlier: 3.669A pdb=" N VAL A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.950A pdb=" N ASP A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 341 removed outlier: 3.518A pdb=" N GLU A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 377 through 384 removed outlier: 3.568A pdb=" N PHE A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 427 removed outlier: 3.750A pdb=" N LYS A 414 " --> pdb=" O THR A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 449 Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 466 through 471 removed outlier: 3.770A pdb=" N ILE A 470 " --> pdb=" O ARG A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 484 through 488 Processing helix chain 'A' and resid 515 through 525 removed outlier: 3.581A pdb=" N ASP A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 550 Processing helix chain 'A' and resid 571 through 619 removed outlier: 3.923A pdb=" N SER A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU A 603 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLN A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 643 removed outlier: 3.739A pdb=" N VAL A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.766A pdb=" N LEU A 657 " --> pdb=" O LYS A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 680 through 704 removed outlier: 4.603A pdb=" N ARG A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 738 removed outlier: 3.742A pdb=" N ARG A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN A 736 " --> pdb=" O ASP A 732 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY A 737 " --> pdb=" O GLN A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 743 removed outlier: 3.749A pdb=" N ALA A 742 " --> pdb=" O HIS A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 777 removed outlier: 3.570A pdb=" N GLU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 9 Processing helix chain 'Y' and resid 11 through 31 removed outlier: 3.915A pdb=" N GLY Y 31 " --> pdb=" O VAL Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 47 removed outlier: 3.631A pdb=" N LEU Y 44 " --> pdb=" O ASN Y 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 74 through 88 Processing helix chain 'Y' and resid 92 through 102 removed outlier: 3.865A pdb=" N ALA Y 96 " --> pdb=" O VAL Y 92 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY Y 102 " --> pdb=" O TRP Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 135 removed outlier: 3.868A pdb=" N LYS Y 108 " --> pdb=" O MET Y 104 " (cutoff:3.500A) Processing helix chain 'Y' and resid 148 through 174 removed outlier: 4.095A pdb=" N ILE Y 152 " --> pdb=" O THR Y 148 " (cutoff:3.500A) Processing helix chain 'Y' and resid 177 through 188 removed outlier: 3.694A pdb=" N ILE Y 181 " --> pdb=" O ASN Y 177 " (cutoff:3.500A) Processing helix chain 'Y' and resid 190 through 202 removed outlier: 3.734A pdb=" N THR Y 202 " --> pdb=" O ILE Y 198 " (cutoff:3.500A) Processing helix chain 'Y' and resid 214 through 236 Processing helix chain 'Y' and resid 271 through 289 removed outlier: 3.833A pdb=" N ILE Y 275 " --> pdb=" O VAL Y 271 " (cutoff:3.500A) Proline residue: Y 284 - end of helix Processing helix chain 'Y' and resid 294 through 304 removed outlier: 3.905A pdb=" N LEU Y 298 " --> pdb=" O ASN Y 294 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TRP Y 299 " --> pdb=" O ASP Y 295 " (cutoff:3.500A) Processing helix chain 'Y' and resid 310 through 331 Processing helix chain 'Y' and resid 332 through 343 removed outlier: 3.588A pdb=" N GLN Y 343 " --> pdb=" O ASN Y 339 " (cutoff:3.500A) Processing helix chain 'Y' and resid 354 through 381 removed outlier: 4.734A pdb=" N VAL Y 370 " --> pdb=" O ARG Y 366 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY Y 371 " --> pdb=" O LEU Y 367 " (cutoff:3.500A) Processing helix chain 'Y' and resid 382 through 390 removed outlier: 4.143A pdb=" N PHE Y 388 " --> pdb=" O PHE Y 384 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN Y 390 " --> pdb=" O VAL Y 386 " (cutoff:3.500A) Processing helix chain 'Y' and resid 399 through 418 removed outlier: 3.867A pdb=" N VAL Y 405 " --> pdb=" O SER Y 401 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY Y 407 " --> pdb=" O LEU Y 403 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN Y 415 " --> pdb=" O GLU Y 411 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 424 Processing helix chain 'E' and resid 3 through 15 removed outlier: 4.276A pdb=" N LYS E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 59 removed outlier: 4.138A pdb=" N LEU E 57 " --> pdb=" O GLN E 53 " (cutoff:3.500A) Processing helix chain 'V' and resid 86 through 90 removed outlier: 3.691A pdb=" N THR V 90 " --> pdb=" O PRO V 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 20 removed outlier: 3.971A pdb=" N LEU B 13 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE B 16 " --> pdb=" O ALA B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 24 removed outlier: 3.517A pdb=" N GLN B 24 " --> pdb=" O SER B 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 21 through 24' Processing helix chain 'G' and resid 57 through 62 removed outlier: 4.611A pdb=" N THR G 62 " --> pdb=" O PRO G 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.577A pdb=" N ARG C 31 " --> pdb=" O PRO C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.410A pdb=" N ILE A 97 " --> pdb=" O VAL A 390 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 154 removed outlier: 6.798A pdb=" N GLY A 153 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N THR A 176 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N HIS A 125 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 226 removed outlier: 6.651A pdb=" N LEU A 221 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR A 354 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 223 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 253 removed outlier: 3.697A pdb=" N GLN A 260 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 258 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 309 Processing sheet with id=AA6, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AA7, first strand: chain 'A' and resid 406 through 407 removed outlier: 6.197A pdb=" N LEU A 406 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 480 through 483 removed outlier: 6.142A pdb=" N LEU A 433 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 238 through 242 Processing sheet with id=AB1, first strand: chain 'V' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'V' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'V' and resid 34 through 37 removed outlier: 6.923A pdb=" N MET V 34 " --> pdb=" O ARG V 50 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG V 50 " --> pdb=" O MET V 34 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TRP V 36 " --> pdb=" O VAL V 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 12 through 22 removed outlier: 5.887A pdb=" N ASN G 149 " --> pdb=" O LYS G 166 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LYS G 166 " --> pdb=" O ASN G 149 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASN G 121 " --> pdb=" O PRO G 13 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU G 15 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE G 123 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLU G 17 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU G 125 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP G 19 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N GLY G 127 " --> pdb=" O ASP G 19 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASP G 21 " --> pdb=" O GLY G 127 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.749A pdb=" N MET C 34 " --> pdb=" O MET C 51 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY C 50 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 58 " --> pdb=" O GLY C 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 11 through 12 708 hydrogen bonds defined for protein. 2033 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: 4.81 Time building geometry restraints manager: 4.59 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: 2988 1.32 - 1.45: 3203 1.45 - 1.57: 7774 1.57 - 1.69: 9 1.69 - 1.81: 123 Bond restraints: 14097 Sorted by residual: bond pdb=" F3 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.769 -0.293 2.00e-02 2.50e+03 2.14e+02 bond pdb=" F1 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.761 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" F2 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.756 -0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" C19 PGV Y 502 " pdb=" O03 PGV Y 502 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C19 PGV Y 501 " pdb=" O03 PGV Y 501 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.99e+01 ... (remaining 14092 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 18402 3.60 - 7.21: 535 7.21 - 10.81: 88 10.81 - 14.41: 11 14.41 - 18.01: 1 Bond angle restraints: 19037 Sorted by residual: angle pdb=" C GLN Y 65 " pdb=" CA GLN Y 65 " pdb=" CB GLN Y 65 " ideal model delta sigma weight residual 111.22 100.53 10.69 1.23e+00 6.61e-01 7.56e+01 angle pdb=" N LEU A 666 " pdb=" CA LEU A 666 " pdb=" C LEU A 666 " ideal model delta sigma weight residual 110.88 120.21 -9.33 1.28e+00 6.10e-01 5.31e+01 angle pdb=" N GLU A 668 " pdb=" CA GLU A 668 " pdb=" CB GLU A 668 " ideal model delta sigma weight residual 110.80 100.14 10.66 1.49e+00 4.50e-01 5.12e+01 angle pdb=" C ILE Y 275 " pdb=" N PHE Y 276 " pdb=" CA PHE Y 276 " ideal model delta sigma weight residual 122.38 110.27 12.11 1.81e+00 3.05e-01 4.48e+01 angle pdb=" N GLY Y 251 " pdb=" CA GLY Y 251 " pdb=" C GLY Y 251 " ideal model delta sigma weight residual 115.36 124.00 -8.64 1.33e+00 5.65e-01 4.22e+01 ... (remaining 19032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 8348 35.31 - 70.62: 121 70.62 - 105.93: 4 105.93 - 141.24: 2 141.24 - 176.54: 5 Dihedral angle restraints: 8480 sinusoidal: 3474 harmonic: 5006 Sorted by residual: dihedral pdb=" CA VAL V 101 " pdb=" C VAL V 101 " pdb=" N MET V 102 " pdb=" CA MET V 102 " ideal model delta harmonic sigma weight residual -180.00 -112.12 -67.88 0 5.00e+00 4.00e-02 1.84e+02 dihedral pdb=" CA GLY V 42 " pdb=" C GLY V 42 " pdb=" N LYS V 43 " pdb=" CA LYS V 43 " ideal model delta harmonic sigma weight residual -180.00 -133.68 -46.32 0 5.00e+00 4.00e-02 8.58e+01 dihedral pdb=" CA ARG V 44 " pdb=" C ARG V 44 " pdb=" N ARG V 45 " pdb=" CA ARG V 45 " ideal model delta harmonic sigma weight residual -180.00 -138.29 -41.71 0 5.00e+00 4.00e-02 6.96e+01 ... (remaining 8477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1844 0.118 - 0.237: 261 0.237 - 0.355: 17 0.355 - 0.474: 5 0.474 - 0.592: 2 Chirality restraints: 2129 Sorted by residual: chirality pdb=" CA ARG Y 252 " pdb=" N ARG Y 252 " pdb=" C ARG Y 252 " pdb=" CB ARG Y 252 " both_signs ideal model delta sigma weight residual False 2.51 3.10 -0.59 2.00e-01 2.50e+01 8.76e+00 chirality pdb=" CA GLU Y 250 " pdb=" N GLU Y 250 " pdb=" C GLU Y 250 " pdb=" CB GLU Y 250 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.35e+00 chirality pdb=" CA ASN C 82A" pdb=" N ASN C 82A" pdb=" C ASN C 82A" pdb=" CB ASN C 82A" both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.98e+00 ... (remaining 2126 not shown) Planarity restraints: 2445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE G 64 " -0.071 2.00e-02 2.50e+03 1.39e-01 1.94e+02 pdb=" C PHE G 64 " 0.241 2.00e-02 2.50e+03 pdb=" O PHE G 64 " -0.097 2.00e-02 2.50e+03 pdb=" N GYS G 66 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG V 44 " 0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C ARG V 44 " -0.070 2.00e-02 2.50e+03 pdb=" O ARG V 44 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG V 45 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 290 " 0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C ILE A 290 " -0.057 2.00e-02 2.50e+03 pdb=" O ILE A 290 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 291 " 0.019 2.00e-02 2.50e+03 ... (remaining 2442 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 7 2.24 - 2.90: 5513 2.90 - 3.57: 19597 3.57 - 4.23: 31636 4.23 - 4.90: 54179 Nonbonded interactions: 110932 Sorted by model distance: nonbonded pdb=" NH2 ARG A 528 " pdb=" F1 BEF A1002 " model vdw 1.574 3.070 nonbonded pdb=" O ASN A 662 " pdb=" O ASP A 667 " model vdw 1.787 3.040 nonbonded pdb=" NH2 ARG A 525 " pdb=" F2 BEF A1002 " model vdw 1.823 3.070 nonbonded pdb=" NZ LYS Y 354 " pdb=" OE2 GLU Y 358 " model vdw 1.882 3.120 nonbonded pdb=" O GLN Y 65 " pdb=" CD GLN Y 65 " model vdw 2.045 3.270 ... (remaining 110927 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 35.370 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 0.016 0.293 14102 Z= 0.672 Angle : 1.485 18.015 19045 Z= 0.794 Chirality : 0.083 0.592 2129 Planarity : 0.009 0.072 2444 Dihedral : 13.871 176.545 5264 Min Nonbonded Distance : 1.574 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.96 % Favored : 90.92 % Rotamer: Outliers : 1.02 % Allowed : 7.12 % Favored : 91.86 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -4.38 (0.16), residues: 1719 helix: -2.86 (0.13), residues: 776 sheet: -2.03 (0.29), residues: 270 loop : -3.14 (0.20), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.005 TRP G 57 HIS 0.026 0.004 HIS Y 424 PHE 0.049 0.006 PHE A 203 TYR 0.051 0.005 TYR A 174 ARG 0.022 0.002 ARG C 56 Details of bonding type rmsd link_TRANS : bond 0.10153 ( 1) link_TRANS : angle 7.55383 ( 2) hydrogen bonds : bond 0.13092 ( 703) hydrogen bonds : angle 7.20748 ( 2033) SS BOND : bond 0.01768 ( 3) SS BOND : angle 2.62095 ( 6) covalent geometry : bond 0.01579 (14097) covalent geometry : angle 1.48264 (19037) Misc. bond : bond 0.00102 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 417 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8559 (mt) cc_final: 0.8358 (mt) REVERT: A 501 GLU cc_start: 0.8076 (mp0) cc_final: 0.7694 (mp0) REVERT: A 539 LEU cc_start: 0.8549 (mm) cc_final: 0.8245 (mp) REVERT: A 543 ASP cc_start: 0.8185 (t70) cc_final: 0.7928 (t0) REVERT: A 549 PHE cc_start: 0.7942 (m-80) cc_final: 0.7604 (m-80) REVERT: A 555 MET cc_start: 0.7244 (mmt) cc_final: 0.6863 (mmm) REVERT: A 601 ASP cc_start: 0.7630 (t0) cc_final: 0.7210 (t0) REVERT: Y 67 PHE cc_start: 0.8333 (t80) cc_final: 0.8024 (t80) REVERT: Y 139 MET cc_start: 0.8134 (pmt) cc_final: 0.7636 (pmt) REVERT: Y 142 GLN cc_start: 0.6868 (pp30) cc_final: 0.6646 (pp30) REVERT: V 64 LYS cc_start: 0.7349 (tptt) cc_final: 0.7090 (tptp) REVERT: V 103 SER cc_start: 0.8691 (m) cc_final: 0.8418 (p) REVERT: G 18 LEU cc_start: 0.7640 (tt) cc_final: 0.7197 (tp) REVERT: G 55 VAL cc_start: 0.7963 (m) cc_final: 0.7731 (p) REVERT: G 123 ILE cc_start: 0.8021 (mp) cc_final: 0.7447 (mp) REVERT: C 81 GLN cc_start: 0.6739 (mm110) cc_final: 0.6291 (mm-40) REVERT: C 98 PHE cc_start: 0.6912 (m-10) cc_final: 0.6615 (m-80) REVERT: C 101 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6681 (tm-30) outliers start: 15 outliers final: 2 residues processed: 427 average time/residue: 0.2812 time to fit residues: 171.1629 Evaluate side-chains 268 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 266 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 602 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 0.0670 chunk 99 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 157 ASN A 188 ASN A 283 HIS A 287 ASN A 297 HIS A 359 ASN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 HIS A 529 GLN A 613 GLN A 747 ASN A 753 GLN Y 101 GLN Y 142 GLN Y 143 ASN ** Y 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 267 ASN Y 308 HIS Y 355 ASN Y 424 HIS G 25 HIS C 76 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.160205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.120316 restraints weight = 31509.372| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.95 r_work: 0.3212 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14102 Z= 0.160 Angle : 0.776 9.631 19045 Z= 0.402 Chirality : 0.048 0.322 2129 Planarity : 0.006 0.053 2444 Dihedral : 10.765 164.289 1973 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.00 % Allowed : 13.09 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.67 (0.19), residues: 1719 helix: -0.97 (0.18), residues: 768 sheet: -1.64 (0.29), residues: 273 loop : -2.69 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 103 HIS 0.007 0.001 HIS G 181 PHE 0.031 0.002 PHE Y 276 TYR 0.023 0.002 TYR V 96 ARG 0.005 0.001 ARG A 607 Details of bonding type rmsd link_TRANS : bond 0.00223 ( 1) link_TRANS : angle 0.10795 ( 2) hydrogen bonds : bond 0.04685 ( 703) hydrogen bonds : angle 5.61427 ( 2033) SS BOND : bond 0.00506 ( 3) SS BOND : angle 2.59385 ( 6) covalent geometry : bond 0.00344 (14097) covalent geometry : angle 0.77514 (19037) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 325 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.8593 (mmm) cc_final: 0.8150 (mmm) REVERT: A 187 ASP cc_start: 0.8032 (m-30) cc_final: 0.7827 (m-30) REVERT: A 384 ILE cc_start: 0.8732 (mm) cc_final: 0.8432 (mt) REVERT: A 469 GLN cc_start: 0.8307 (pp30) cc_final: 0.8050 (pt0) REVERT: A 501 GLU cc_start: 0.8424 (mp0) cc_final: 0.7767 (mp0) REVERT: A 515 SER cc_start: 0.8888 (t) cc_final: 0.8487 (m) REVERT: A 557 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8216 (mtm) REVERT: A 573 MET cc_start: 0.4933 (tpp) cc_final: 0.4617 (tpt) REVERT: A 601 ASP cc_start: 0.8250 (t0) cc_final: 0.7723 (t0) REVERT: A 733 GLN cc_start: 0.8896 (tm-30) cc_final: 0.8055 (tt0) REVERT: Y 104 MET cc_start: 0.7242 (tpp) cc_final: 0.6474 (mmt) REVERT: Y 139 MET cc_start: 0.7740 (pmt) cc_final: 0.7192 (pmt) REVERT: Y 142 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6508 (pp30) REVERT: V 6 GLU cc_start: 0.6366 (mp0) cc_final: 0.5929 (mp0) REVERT: V 38 ARG cc_start: 0.7044 (ttm110) cc_final: 0.6465 (ttm170) REVERT: V 39 GLN cc_start: 0.7643 (pp30) cc_final: 0.6910 (tm-30) REVERT: V 64 LYS cc_start: 0.7287 (tptt) cc_final: 0.6907 (tptp) REVERT: V 94 TYR cc_start: 0.7026 (m-80) cc_final: 0.6625 (m-80) REVERT: G 16 VAL cc_start: 0.8294 (t) cc_final: 0.8065 (m) REVERT: G 88 MET cc_start: 0.6802 (mmt) cc_final: 0.6594 (tpp) REVERT: G 109 ARG cc_start: 0.6780 (tpm170) cc_final: 0.6439 (tpm170) REVERT: G 166 LYS cc_start: 0.6952 (mppt) cc_final: 0.6565 (mmtm) REVERT: G 200 TYR cc_start: 0.6170 (p90) cc_final: 0.5717 (p90) REVERT: C 34 MET cc_start: 0.8096 (mmm) cc_final: 0.7807 (mmm) REVERT: C 56 ARG cc_start: 0.6895 (ptm-80) cc_final: 0.6449 (ptm-80) REVERT: C 72 ASP cc_start: 0.7674 (p0) cc_final: 0.7253 (p0) outliers start: 59 outliers final: 26 residues processed: 359 average time/residue: 0.2567 time to fit residues: 134.5646 Evaluate side-chains 286 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 258 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 776 MET Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 24 MET Chi-restraints excluded: chain Y residue 142 GLN Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 413 MET Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 96 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 80 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 18 optimal weight: 0.0970 chunk 85 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 158 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 101 GLN Y 143 ASN ** Y 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.157158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.121177 restraints weight = 23264.184| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.78 r_work: 0.3207 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14102 Z= 0.151 Angle : 0.711 8.915 19045 Z= 0.368 Chirality : 0.046 0.295 2129 Planarity : 0.005 0.063 2444 Dihedral : 9.724 168.520 1970 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.93 % Allowed : 14.79 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.86 (0.19), residues: 1719 helix: -0.12 (0.19), residues: 761 sheet: -1.36 (0.29), residues: 280 loop : -2.45 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 103 HIS 0.006 0.001 HIS G 181 PHE 0.032 0.002 PHE Y 276 TYR 0.024 0.002 TYR V 96 ARG 0.006 0.000 ARG A 75 Details of bonding type rmsd link_TRANS : bond 0.00104 ( 1) link_TRANS : angle 0.33828 ( 2) hydrogen bonds : bond 0.04298 ( 703) hydrogen bonds : angle 5.19803 ( 2033) SS BOND : bond 0.00532 ( 3) SS BOND : angle 4.97752 ( 6) covalent geometry : bond 0.00333 (14097) covalent geometry : angle 0.70514 (19037) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 284 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8685 (mp) cc_final: 0.8405 (mp) REVERT: A 141 MET cc_start: 0.8838 (mmm) cc_final: 0.8074 (mmm) REVERT: A 250 TYR cc_start: 0.8626 (p90) cc_final: 0.8390 (p90) REVERT: A 384 ILE cc_start: 0.8932 (mm) cc_final: 0.8655 (mt) REVERT: A 427 MET cc_start: 0.7858 (ppp) cc_final: 0.7430 (ppp) REVERT: A 515 SER cc_start: 0.9212 (t) cc_final: 0.8732 (m) REVERT: A 539 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8457 (mm) REVERT: A 601 ASP cc_start: 0.8544 (t0) cc_final: 0.7941 (t0) REVERT: A 645 ARG cc_start: 0.7772 (tmt170) cc_final: 0.7428 (tpt170) REVERT: A 702 GLN cc_start: 0.8199 (pp30) cc_final: 0.7269 (tp40) REVERT: A 733 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8257 (tt0) REVERT: A 755 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7780 (tp30) REVERT: A 776 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7801 (mtt) REVERT: Y 101 GLN cc_start: 0.5132 (OUTLIER) cc_final: 0.4800 (pp30) REVERT: Y 104 MET cc_start: 0.7383 (tpp) cc_final: 0.6656 (mmt) REVERT: Y 139 MET cc_start: 0.7779 (pmt) cc_final: 0.7216 (pmt) REVERT: Y 142 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6688 (pp30) REVERT: V 6 GLU cc_start: 0.6854 (mp0) cc_final: 0.6641 (mp0) REVERT: V 38 ARG cc_start: 0.7169 (ttm170) cc_final: 0.6724 (ttm110) REVERT: V 39 GLN cc_start: 0.7624 (pp30) cc_final: 0.6990 (tm-30) REVERT: V 61 ASP cc_start: 0.6862 (m-30) cc_final: 0.6640 (m-30) REVERT: V 64 LYS cc_start: 0.7348 (tptt) cc_final: 0.6990 (tptp) REVERT: V 94 TYR cc_start: 0.7003 (m-80) cc_final: 0.6744 (m-80) REVERT: G 78 MET cc_start: 0.6059 (ptp) cc_final: 0.5705 (pmm) REVERT: G 88 MET cc_start: 0.6947 (mmt) cc_final: 0.6564 (tpt) REVERT: G 166 LYS cc_start: 0.7083 (mppt) cc_final: 0.6559 (mmtm) REVERT: G 200 TYR cc_start: 0.6185 (p90) cc_final: 0.5812 (p90) REVERT: C 51 MET cc_start: 0.7664 (tmm) cc_final: 0.7456 (tmm) REVERT: C 56 ARG cc_start: 0.6907 (ptm-80) cc_final: 0.6492 (ptm-80) REVERT: C 98 PHE cc_start: 0.7554 (m-80) cc_final: 0.7324 (m-80) REVERT: C 101 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7163 (tm-30) outliers start: 58 outliers final: 39 residues processed: 318 average time/residue: 0.2683 time to fit residues: 124.6937 Evaluate side-chains 300 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 256 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 776 MET Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 24 MET Chi-restraints excluded: chain Y residue 101 GLN Chi-restraints excluded: chain Y residue 141 ILE Chi-restraints excluded: chain Y residue 142 GLN Chi-restraints excluded: chain Y residue 182 ILE Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 305 ASP Chi-restraints excluded: chain Y residue 368 THR Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain G residue 64 PHE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 96 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 45 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 90 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 238 ASN ** Y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 143 ASN Y 177 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.155727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.120737 restraints weight = 30302.914| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 4.74 r_work: 0.3068 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14102 Z= 0.148 Angle : 0.685 8.178 19045 Z= 0.353 Chirality : 0.046 0.266 2129 Planarity : 0.004 0.058 2444 Dihedral : 9.084 170.166 1970 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.14 % Allowed : 16.62 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.46 (0.20), residues: 1719 helix: 0.24 (0.19), residues: 770 sheet: -1.26 (0.28), residues: 285 loop : -2.25 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 103 HIS 0.005 0.001 HIS G 181 PHE 0.032 0.002 PHE Y 276 TYR 0.022 0.002 TYR V 96 ARG 0.006 0.000 ARG E 13 Details of bonding type rmsd link_TRANS : bond 0.00171 ( 1) link_TRANS : angle 0.28966 ( 2) hydrogen bonds : bond 0.04072 ( 703) hydrogen bonds : angle 4.94659 ( 2033) SS BOND : bond 0.00405 ( 3) SS BOND : angle 2.63094 ( 6) covalent geometry : bond 0.00330 (14097) covalent geometry : angle 0.68361 (19037) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 279 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8271 (mp) REVERT: A 427 MET cc_start: 0.8105 (ppp) cc_final: 0.7603 (ppp) REVERT: A 515 SER cc_start: 0.9422 (t) cc_final: 0.8934 (m) REVERT: A 645 ARG cc_start: 0.7905 (tmt170) cc_final: 0.7544 (tpt170) REVERT: A 680 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6360 (tt0) REVERT: A 702 GLN cc_start: 0.8245 (pp30) cc_final: 0.7680 (tp40) REVERT: A 729 ASP cc_start: 0.9035 (t70) cc_final: 0.8174 (m-30) REVERT: A 733 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8418 (tt0) REVERT: A 755 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7969 (tp30) REVERT: Y 77 TYR cc_start: 0.7914 (t80) cc_final: 0.7708 (t80) REVERT: Y 104 MET cc_start: 0.7543 (tpp) cc_final: 0.6472 (mmt) REVERT: Y 142 GLN cc_start: 0.6952 (pp30) cc_final: 0.6674 (pp30) REVERT: Y 301 ARG cc_start: 0.8345 (mtm110) cc_final: 0.8077 (mtm-85) REVERT: Y 417 GLU cc_start: 0.8561 (pp20) cc_final: 0.8319 (pp20) REVERT: V 38 ARG cc_start: 0.7292 (ttm170) cc_final: 0.6987 (ttm110) REVERT: V 39 GLN cc_start: 0.7477 (pp30) cc_final: 0.7230 (tm-30) REVERT: V 64 LYS cc_start: 0.7364 (tptt) cc_final: 0.6973 (tptp) REVERT: V 97 TYR cc_start: 0.8011 (p90) cc_final: 0.7797 (p90) REVERT: V 102 MET cc_start: 0.7239 (pmm) cc_final: 0.7004 (pmm) REVERT: V 114 THR cc_start: 0.6896 (OUTLIER) cc_final: 0.6676 (p) REVERT: G 78 MET cc_start: 0.6199 (ptp) cc_final: 0.5344 (pmm) REVERT: G 88 MET cc_start: 0.6862 (mmt) cc_final: 0.6502 (tpt) REVERT: G 123 ILE cc_start: 0.7825 (mp) cc_final: 0.7392 (mp) REVERT: G 166 LYS cc_start: 0.7139 (mppt) cc_final: 0.6498 (mmtm) REVERT: G 200 TYR cc_start: 0.6133 (p90) cc_final: 0.5793 (p90) REVERT: C 51 MET cc_start: 0.7626 (tmm) cc_final: 0.7383 (tmm) REVERT: C 56 ARG cc_start: 0.6965 (ptm-80) cc_final: 0.6306 (ptm-80) REVERT: C 101 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7207 (tm-30) REVERT: C 103 TRP cc_start: 0.7672 (m100) cc_final: 0.7372 (m100) outliers start: 61 outliers final: 39 residues processed: 319 average time/residue: 0.2633 time to fit residues: 121.0964 Evaluate side-chains 296 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 254 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 24 MET Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 305 ASP Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain Y residue 413 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 96 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.3711 > 50: distance: 33 - 195: 11.607 distance: 142 - 147: 4.146 distance: 147 - 148: 7.350 distance: 148 - 149: 4.182 distance: 148 - 151: 11.297 distance: 149 - 150: 7.774 distance: 149 - 154: 6.798 distance: 151 - 152: 9.800 distance: 151 - 153: 13.152 distance: 154 - 155: 9.691 distance: 154 - 311: 10.086 distance: 155 - 156: 7.738 distance: 155 - 158: 8.337 distance: 156 - 157: 7.276 distance: 156 - 159: 6.198 distance: 157 - 308: 10.993 distance: 159 - 160: 8.215 distance: 160 - 161: 12.749 distance: 160 - 163: 7.675 distance: 161 - 162: 8.921 distance: 161 - 166: 7.188 distance: 163 - 164: 5.008 distance: 163 - 165: 11.620 distance: 166 - 167: 10.664 distance: 166 - 295: 12.353 distance: 167 - 168: 7.901 distance: 167 - 170: 14.096 distance: 168 - 169: 20.150 distance: 168 - 178: 7.144 distance: 169 - 292: 18.876 distance: 170 - 171: 7.022 distance: 171 - 172: 14.600 distance: 171 - 173: 33.771 distance: 173 - 175: 5.346 distance: 174 - 176: 22.443 distance: 175 - 176: 26.815 distance: 176 - 177: 8.656 distance: 178 - 179: 9.316 distance: 179 - 180: 10.768 distance: 179 - 182: 19.671 distance: 180 - 181: 8.674 distance: 180 - 190: 12.414 distance: 182 - 183: 5.308 distance: 183 - 184: 11.327 distance: 183 - 185: 21.887 distance: 184 - 186: 8.800 distance: 185 - 187: 6.689 distance: 186 - 188: 18.989 distance: 187 - 188: 16.680 distance: 188 - 189: 10.110 distance: 190 - 191: 4.626 distance: 191 - 192: 16.907 distance: 191 - 194: 18.246 distance: 192 - 193: 21.701 distance: 192 - 196: 26.074 distance: 194 - 195: 17.574 distance: 196 - 197: 25.295 distance: 197 - 198: 7.482 distance: 197 - 200: 20.097 distance: 198 - 199: 11.659 distance: 198 - 208: 11.951 distance: 200 - 201: 21.089 distance: 201 - 202: 8.744 distance: 201 - 203: 35.369 distance: 202 - 204: 11.575 distance: 203 - 205: 12.004 distance: 204 - 206: 25.720 distance: 205 - 206: 18.676 distance: 206 - 207: 12.736 distance: 209 - 210: 27.014 distance: 209 - 212: 16.739 distance: 212 - 213: 16.425 distance: 213 - 214: 7.159 distance: 213 - 215: 9.590 distance: 214 - 216: 5.018 distance: 215 - 217: 9.742 distance: 217 - 218: 8.552 distance: 218 - 219: 7.566 distance: 220 - 221: 42.056 distance: 221 - 222: 14.289 distance: 224 - 225: 24.028 distance: 225 - 226: 10.966 distance: 226 - 227: 30.645 distance: 226 - 228: 31.401 distance: 229 - 230: 24.409 distance: 230 - 231: 3.246 distance: 230 - 233: 8.524 distance: 231 - 232: 7.767 distance: 231 - 240: 20.780 distance: 233 - 234: 23.685 distance: 234 - 235: 14.707 distance: 235 - 236: 6.390 distance: 236 - 237: 20.995 distance: 237 - 238: 29.166 distance: 237 - 239: 13.693