Starting phenix.real_space_refine on Thu Nov 16 13:34:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rku_4910/11_2023/6rku_4910_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rku_4910/11_2023/6rku_4910.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rku_4910/11_2023/6rku_4910_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rku_4910/11_2023/6rku_4910_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rku_4910/11_2023/6rku_4910_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rku_4910/11_2023/6rku_4910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rku_4910/11_2023/6rku_4910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rku_4910/11_2023/6rku_4910_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rku_4910/11_2023/6rku_4910_updated.pdb" } resolution = 4.0 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= 0.002 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: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 54 5.16 5 C 9570 2.51 5 N 2762 2.21 5 O 3076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 46": "NH1" <-> "NH2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 433": "NH1" <-> "NH2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "B ARG 438": "NH1" <-> "NH2" Residue "B ARG 489": "NH1" <-> "NH2" Residue "B ARG 516": "NH1" <-> "NH2" Residue "B ARG 667": "NH1" <-> "NH2" Residue "B ARG 689": "NH1" <-> "NH2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ARG 433": "NH1" <-> "NH2" Residue "C ARG 490": "NH1" <-> "NH2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "D ARG 438": "NH1" <-> "NH2" Residue "D ARG 489": "NH1" <-> "NH2" Residue "D ARG 516": "NH1" <-> "NH2" Residue "D ARG 667": "NH1" <-> "NH2" Residue "D ARG 689": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 15526 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4022 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain breaks: 2 Chain: "B" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3052 Classifications: {'peptide': 381} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 363} Chain breaks: 1 Chain: "C" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4022 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain breaks: 2 Chain: "D" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3052 Classifications: {'peptide': 381} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 363} Chain breaks: 1 Chain: "F" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "E" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "G" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 368 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "H" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 368 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "G" Number of atoms: 66 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 33 Unusual residues: {'JHN': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 33 Unusual residues: {'JHN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 AJHN G 101 " occ=0.50 ... (64 atoms not shown) pdb=" O3 BJHN G 101 " occ=0.50 Time building chain proxies: 8.43, per 1000 atoms: 0.54 Number of scatterers: 15526 At special positions: 0 Unit cell: (161.04, 132.88, 124.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 64 15.00 O 3076 8.00 N 2762 7.00 C 9570 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: 6.15 Conformation dependent library (CDL) restraints added in 2.7 seconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3340 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 16 sheets defined 43.9% alpha, 10.0% beta 32 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 6.91 Creating SS restraints... Processing helix chain 'A' and resid 14 through 31 removed outlier: 3.594A pdb=" N SER A 20 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR A 21 " --> pdb=" O LYS A 18 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 22 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 29 " --> pdb=" O MET A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 55 Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 83 through 93 removed outlier: 3.509A pdb=" N ALA A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 131 through 134 No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 165 through 168 No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 314 through 323 Processing helix chain 'A' and resid 347 through 388 removed outlier: 3.658A pdb=" N ALA A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 399 Processing helix chain 'A' and resid 403 through 412 Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 452 through 459 Processing helix chain 'A' and resid 470 through 493 Processing helix chain 'A' and resid 495 through 513 Processing helix chain 'B' and resid 425 through 435 removed outlier: 3.881A pdb=" N GLY B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 501 through 517 Processing helix chain 'B' and resid 519 through 523 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 578 through 599 removed outlier: 4.590A pdb=" N ARG B 599 " --> pdb=" O ASN B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 610 removed outlier: 4.289A pdb=" N ILE B 610 " --> pdb=" O LEU B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 620 removed outlier: 3.515A pdb=" N LEU B 620 " --> pdb=" O GLU B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 617 through 620' Processing helix chain 'B' and resid 623 through 640 Processing helix chain 'B' and resid 679 through 683 Processing helix chain 'B' and resid 685 through 700 removed outlier: 3.943A pdb=" N LEU B 700 " --> pdb=" O LYS B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 731 Processing helix chain 'B' and resid 742 through 744 No H-bonds generated for 'chain 'B' and resid 742 through 744' Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 773 through 778 removed outlier: 4.498A pdb=" N THR B 778 " --> pdb=" O ASP B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 786 Processing helix chain 'C' and resid 14 through 31 removed outlier: 3.593A pdb=" N SER C 20 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR C 21 " --> pdb=" O LYS C 18 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 22 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE C 29 " --> pdb=" O MET C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 55 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 83 through 93 removed outlier: 3.509A pdb=" N ALA C 93 " --> pdb=" O ILE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 131 through 134 No H-bonds generated for 'chain 'C' and resid 131 through 134' Processing helix chain 'C' and resid 165 through 168 No H-bonds generated for 'chain 'C' and resid 165 through 168' Processing helix chain 'C' and resid 187 through 199 Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 226 through 234 Processing helix chain 'C' and resid 270 through 283 Processing helix chain 'C' and resid 314 through 323 Processing helix chain 'C' and resid 347 through 388 removed outlier: 3.657A pdb=" N ALA C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 399 Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 419 through 421 No H-bonds generated for 'chain 'C' and resid 419 through 421' Processing helix chain 'C' and resid 452 through 459 Processing helix chain 'C' and resid 470 through 493 Processing helix chain 'C' and resid 495 through 513 Processing helix chain 'D' and resid 425 through 435 removed outlier: 3.880A pdb=" N GLY D 430 " --> pdb=" O ASP D 426 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER D 431 " --> pdb=" O SER D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 471 Processing helix chain 'D' and resid 501 through 517 Processing helix chain 'D' and resid 519 through 523 Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 578 through 599 removed outlier: 4.591A pdb=" N ARG D 599 " --> pdb=" O ASN D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 610 removed outlier: 4.289A pdb=" N ILE D 610 " --> pdb=" O LEU D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 620 removed outlier: 3.516A pdb=" N LEU D 620 " --> pdb=" O GLU D 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 617 through 620' Processing helix chain 'D' and resid 623 through 640 Processing helix chain 'D' and resid 679 through 683 Processing helix chain 'D' and resid 685 through 700 removed outlier: 3.943A pdb=" N LEU D 700 " --> pdb=" O LYS D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 731 Processing helix chain 'D' and resid 742 through 744 No H-bonds generated for 'chain 'D' and resid 742 through 744' Processing helix chain 'D' and resid 747 through 754 Processing helix chain 'D' and resid 773 through 778 removed outlier: 4.498A pdb=" N THR D 778 " --> pdb=" O ASP D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 781 through 786 Processing sheet with id= A, first strand: chain 'A' and resid 103 through 106 Processing sheet with id= B, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= C, first strand: chain 'A' and resid 237 through 243 removed outlier: 3.511A pdb=" N GLY A 238 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 245 through 250 removed outlier: 3.659A pdb=" N ARG A 245 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU A 263 " --> pdb=" O ARG A 245 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU A 247 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL A 261 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU A 249 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE A 259 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLU A 257 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 304 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU A 306 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA A 291 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 335 through 337 removed outlier: 3.836A pdb=" N ALA A 336 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 441 through 446 removed outlier: 6.445A pdb=" N GLU B 419 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU B 444 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR B 421 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU B 446 " --> pdb=" O TYR B 421 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 423 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 542 through 546 Processing sheet with id= H, first strand: chain 'B' and resid 646 through 653 removed outlier: 3.517A pdb=" N GLN B 646 " --> pdb=" O ARG B 667 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG B 667 " --> pdb=" O GLN B 646 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS B 652 " --> pdb=" O GLU B 661 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 664 " --> pdb=" O TYR B 675 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 103 through 106 Processing sheet with id= J, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= K, first strand: chain 'C' and resid 237 through 243 removed outlier: 3.511A pdb=" N GLY C 238 " --> pdb=" O ILE C 332 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 245 through 250 removed outlier: 3.659A pdb=" N ARG C 245 " --> pdb=" O GLU C 263 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU C 263 " --> pdb=" O ARG C 245 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLU C 247 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL C 261 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU C 249 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE C 259 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLU C 257 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL C 304 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU C 306 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA C 291 " --> pdb=" O GLU C 306 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 335 through 337 removed outlier: 3.836A pdb=" N ALA C 336 " --> pdb=" O LYS C 343 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 441 through 446 removed outlier: 6.445A pdb=" N GLU D 419 " --> pdb=" O ALA D 442 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU D 444 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TYR D 421 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU D 446 " --> pdb=" O TYR D 421 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL D 423 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 542 through 546 Processing sheet with id= P, first strand: chain 'D' and resid 646 through 653 removed outlier: 3.517A pdb=" N GLN D 646 " --> pdb=" O ARG D 667 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG D 667 " --> pdb=" O GLN D 646 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS D 652 " --> pdb=" O GLU D 661 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 664 " --> pdb=" O TYR D 675 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 5.27 Time building geometry restraints manager: 6.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4151 1.33 - 1.45: 2755 1.45 - 1.57: 8792 1.57 - 1.69: 124 1.69 - 1.80: 102 Bond restraints: 15924 Sorted by residual: bond pdb=" C2 BJHN G 101 " pdb=" C3 BJHN G 101 " ideal model delta sigma weight residual 2.160 1.352 0.808 2.00e-02 2.50e+03 1.63e+03 bond pdb=" C2 AJHN G 101 " pdb=" C3 AJHN G 101 " ideal model delta sigma weight residual 2.160 1.352 0.808 2.00e-02 2.50e+03 1.63e+03 bond pdb=" C5 BJHN G 101 " pdb=" C6 BJHN G 101 " ideal model delta sigma weight residual 0.686 1.491 -0.805 2.00e-02 2.50e+03 1.62e+03 bond pdb=" C5 AJHN G 101 " pdb=" C6 AJHN G 101 " ideal model delta sigma weight residual 0.686 1.491 -0.805 2.00e-02 2.50e+03 1.62e+03 bond pdb=" C1 AJHN G 101 " pdb=" C2 AJHN G 101 " ideal model delta sigma weight residual 1.959 1.437 0.522 2.00e-02 2.50e+03 6.81e+02 ... (remaining 15919 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.71: 799 106.71 - 113.54: 8865 113.54 - 120.36: 5992 120.36 - 127.18: 5906 127.18 - 134.01: 240 Bond angle restraints: 21802 Sorted by residual: angle pdb=" C3 BJHN G 101 " pdb=" C4 BJHN G 101 " pdb=" N1 BJHN G 101 " ideal model delta sigma weight residual 17.58 127.01 -109.43 3.00e+00 1.11e-01 1.33e+03 angle pdb=" C3 AJHN G 101 " pdb=" C4 AJHN G 101 " pdb=" N1 AJHN G 101 " ideal model delta sigma weight residual 17.58 126.93 -109.35 3.00e+00 1.11e-01 1.33e+03 angle pdb=" C1 AJHN G 101 " pdb=" N6 AJHN G 101 " pdb=" C23AJHN G 101 " ideal model delta sigma weight residual 29.62 126.11 -96.49 3.00e+00 1.11e-01 1.03e+03 angle pdb=" C1 BJHN G 101 " pdb=" N6 BJHN G 101 " pdb=" C23BJHN G 101 " ideal model delta sigma weight residual 29.62 125.91 -96.29 3.00e+00 1.11e-01 1.03e+03 angle pdb=" C4 AJHN G 101 " pdb=" C24AJHN G 101 " pdb=" N2 AJHN G 101 " ideal model delta sigma weight residual 65.03 129.23 -64.20 3.00e+00 1.11e-01 4.58e+02 ... (remaining 21797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.67: 9255 33.67 - 67.33: 235 67.33 - 100.99: 4 100.99 - 134.66: 14 134.66 - 168.32: 6 Dihedral angle restraints: 9514 sinusoidal: 4338 harmonic: 5176 Sorted by residual: dihedral pdb=" C10BJHN G 101 " pdb=" C11BJHN G 101 " pdb=" N4 BJHN G 101 " pdb=" C14BJHN G 101 " ideal model delta sinusoidal sigma weight residual 113.22 -55.10 168.32 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C10AJHN G 101 " pdb=" C11AJHN G 101 " pdb=" N4 AJHN G 101 " pdb=" C14AJHN G 101 " ideal model delta sinusoidal sigma weight residual 113.22 -55.05 168.27 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" CA GLU B 424 " pdb=" C GLU B 424 " pdb=" N GLY B 425 " pdb=" CA GLY B 425 " ideal model delta harmonic sigma weight residual 180.00 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 9511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.993: 2446 0.993 - 1.986: 0 1.986 - 2.979: 0 2.979 - 3.972: 0 3.972 - 4.965: 2 Chirality restraints: 2448 Sorted by residual: chirality pdb=" C11BJHN G 101 " pdb=" C10BJHN G 101 " pdb=" C12BJHN G 101 " pdb=" N4 BJHN G 101 " both_signs ideal model delta sigma weight residual False -2.58 2.38 -4.97 2.00e-01 2.50e+01 6.16e+02 chirality pdb=" C11AJHN G 101 " pdb=" C10AJHN G 101 " pdb=" C12AJHN G 101 " pdb=" N4 AJHN G 101 " both_signs ideal model delta sigma weight residual False -2.58 2.35 -4.94 2.00e-01 2.50e+01 6.09e+02 chirality pdb=" C7 AJHN G 101 " pdb=" C23AJHN G 101 " pdb=" C8 AJHN G 101 " pdb=" N2 AJHN G 101 " both_signs ideal model delta sigma weight residual False -2.39 -2.77 0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 2445 not shown) Planarity restraints: 2614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BJHN G 101 " 0.052 2.00e-02 2.50e+03 8.16e-02 2.33e+02 pdb=" C2 BJHN G 101 " 0.009 2.00e-02 2.50e+03 pdb=" C23BJHN G 101 " -0.256 2.00e-02 2.50e+03 pdb=" C24BJHN G 101 " 0.019 2.00e-02 2.50e+03 pdb=" C3 BJHN G 101 " -0.028 2.00e-02 2.50e+03 pdb=" C4 BJHN G 101 " -0.026 2.00e-02 2.50e+03 pdb=" C5 BJHN G 101 " -0.029 2.00e-02 2.50e+03 pdb=" C6 BJHN G 101 " 0.027 2.00e-02 2.50e+03 pdb=" C7 BJHN G 101 " 0.039 2.00e-02 2.50e+03 pdb=" N1 BJHN G 101 " -0.057 2.00e-02 2.50e+03 pdb=" N2 BJHN G 101 " 0.038 2.00e-02 2.50e+03 pdb=" N6 BJHN G 101 " 0.059 2.00e-02 2.50e+03 pdb=" O1 BJHN G 101 " 0.080 2.00e-02 2.50e+03 pdb=" O2 BJHN G 101 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 AJHN G 101 " -0.042 2.00e-02 2.50e+03 6.64e-02 1.54e+02 pdb=" C2 AJHN G 101 " -0.005 2.00e-02 2.50e+03 pdb=" C23AJHN G 101 " 0.205 2.00e-02 2.50e+03 pdb=" C24AJHN G 101 " -0.009 2.00e-02 2.50e+03 pdb=" C3 AJHN G 101 " 0.027 2.00e-02 2.50e+03 pdb=" C4 AJHN G 101 " 0.024 2.00e-02 2.50e+03 pdb=" C5 AJHN G 101 " 0.018 2.00e-02 2.50e+03 pdb=" C6 AJHN G 101 " -0.023 2.00e-02 2.50e+03 pdb=" C7 AJHN G 101 " -0.024 2.00e-02 2.50e+03 pdb=" N1 AJHN G 101 " 0.043 2.00e-02 2.50e+03 pdb=" N2 AJHN G 101 " -0.026 2.00e-02 2.50e+03 pdb=" N6 AJHN G 101 " -0.043 2.00e-02 2.50e+03 pdb=" O1 AJHN G 101 " -0.079 2.00e-02 2.50e+03 pdb=" O2 AJHN G 101 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 780 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C LEU B 780 " 0.057 2.00e-02 2.50e+03 pdb=" O LEU B 780 " -0.021 2.00e-02 2.50e+03 pdb=" N MET B 781 " -0.019 2.00e-02 2.50e+03 ... (remaining 2611 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1997 2.75 - 3.29: 14604 3.29 - 3.83: 24155 3.83 - 4.36: 26591 4.36 - 4.90: 45291 Nonbonded interactions: 112638 Sorted by model distance: nonbonded pdb=" O LYS D 538 " pdb=" OG SER D 735 " model vdw 2.215 2.440 nonbonded pdb=" O LYS B 538 " pdb=" OG SER B 735 " model vdw 2.215 2.440 nonbonded pdb=" OE2 GLU B 454 " pdb=" NH1 ARG B 516 " model vdw 2.260 2.520 nonbonded pdb=" OE2 GLU D 454 " pdb=" NH1 ARG D 516 " model vdw 2.260 2.520 nonbonded pdb=" O HIS B 491 " pdb=" ND1 HIS B 526 " model vdw 2.315 2.520 ... (remaining 112633 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 15 through 32) selection = chain 'H' } 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=0.50 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: 0.010 Normalize map: mean=0, sd=1: 2.020 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: 10.010 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 46.440 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 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 : 0.018 0.808 15924 Z= 0.913 Angle : 1.762 109.433 21802 Z= 0.651 Chirality : 0.147 4.965 2448 Planarity : 0.005 0.082 2614 Dihedral : 14.142 168.324 6174 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -2.01 (0.19), residues: 1764 helix: 0.51 (0.17), residues: 818 sheet: -2.18 (0.33), residues: 232 loop : -3.34 (0.19), residues: 714 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.3405 time to fit residues: 156.4170 Evaluate side-chains 131 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.658 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 93 optimal weight: 0.0010 chunk 73 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 319 ASN A 357 HIS A 378 HIS B 652 HIS C 224 ASN C 319 ASN C 339 HIS C 357 HIS C 378 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.195 15924 Z= 0.292 Angle : 1.410 82.709 21802 Z= 0.532 Chirality : 0.041 0.165 2448 Planarity : 0.005 0.050 2614 Dihedral : 16.916 139.003 2630 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.72 % Allowed : 8.62 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -1.14 (0.20), residues: 1764 helix: 1.41 (0.19), residues: 814 sheet: -1.55 (0.39), residues: 198 loop : -3.16 (0.19), residues: 752 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 153 average time/residue: 0.3100 time to fit residues: 69.3934 Evaluate side-chains 124 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 1.573 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1349 time to fit residues: 6.2156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 56 optimal weight: 0.0370 chunk 132 optimal weight: 4.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 HIS ** C 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.200 15924 Z= 0.293 Angle : 1.391 82.670 21802 Z= 0.519 Chirality : 0.040 0.154 2448 Planarity : 0.005 0.051 2614 Dihedral : 16.733 138.498 2630 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.99 % Allowed : 10.15 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1764 helix: 1.70 (0.19), residues: 826 sheet: -1.56 (0.36), residues: 218 loop : -3.05 (0.18), residues: 720 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 113 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 132 average time/residue: 0.2695 time to fit residues: 54.9554 Evaluate side-chains 118 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 1.682 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 2 residues processed: 15 average time/residue: 0.1425 time to fit residues: 6.2792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 175 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 HIS ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.195 15924 Z= 0.331 Angle : 1.400 82.240 21802 Z= 0.526 Chirality : 0.040 0.177 2448 Planarity : 0.005 0.052 2614 Dihedral : 16.633 138.623 2630 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.39 % Allowed : 10.74 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.20), residues: 1764 helix: 1.78 (0.19), residues: 824 sheet: -1.65 (0.37), residues: 198 loop : -2.97 (0.18), residues: 742 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 1.918 Fit side-chains outliers start: 21 outliers final: 14 residues processed: 121 average time/residue: 0.2667 time to fit residues: 50.8439 Evaluate side-chains 113 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 1.785 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1411 time to fit residues: 6.2002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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: 57.7028 > 50: distance: 42 - 47: 16.343 distance: 47 - 48: 4.503 distance: 48 - 49: 8.677 distance: 49 - 50: 18.050 distance: 49 - 51: 10.785 distance: 51 - 52: 20.308 distance: 52 - 53: 11.317 distance: 52 - 55: 13.438 distance: 53 - 54: 10.296 distance: 53 - 59: 7.614 distance: 55 - 56: 3.220 distance: 56 - 57: 10.089 distance: 59 - 60: 11.569 distance: 60 - 61: 4.937 distance: 60 - 63: 10.482 distance: 61 - 62: 10.425 distance: 61 - 70: 16.550 distance: 63 - 64: 6.579 distance: 64 - 66: 40.641 distance: 65 - 67: 3.007 distance: 66 - 68: 7.766 distance: 67 - 69: 12.471 distance: 68 - 69: 29.824 distance: 70 - 71: 10.089 distance: 71 - 72: 11.767 distance: 72 - 73: 26.966 distance: 72 - 74: 12.589 distance: 74 - 75: 13.908 distance: 75 - 76: 12.308 distance: 75 - 78: 8.230 distance: 76 - 77: 25.483 distance: 76 - 80: 13.552 distance: 78 - 79: 24.820 distance: 80 - 81: 10.805 distance: 81 - 82: 27.850 distance: 81 - 84: 22.426 distance: 82 - 83: 23.822 distance: 82 - 88: 16.068 distance: 84 - 85: 18.709 distance: 84 - 86: 17.356 distance: 85 - 87: 27.205 distance: 88 - 89: 12.513 distance: 89 - 90: 43.126 distance: 89 - 92: 8.129 distance: 90 - 91: 13.647 distance: 90 - 96: 34.950 distance: 92 - 93: 4.174 distance: 93 - 94: 17.524 distance: 93 - 95: 41.352 distance: 96 - 97: 25.679 distance: 97 - 98: 13.548 distance: 98 - 99: 18.483 distance: 98 - 100: 28.469 distance: 100 - 101: 9.483 distance: 101 - 102: 21.226 distance: 101 - 104: 16.575 distance: 102 - 103: 12.207 distance: 102 - 108: 5.783 distance: 104 - 105: 28.068 distance: 105 - 106: 18.065 distance: 105 - 107: 19.430 distance: 108 - 109: 8.712 distance: 109 - 110: 8.461 distance: 109 - 112: 15.491 distance: 110 - 111: 21.395 distance: 110 - 114: 28.340 distance: 112 - 113: 11.691