Starting phenix.real_space_refine on Sat Jan 20 06:30:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ain_11799/01_2024/7ain_11799_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ain_11799/01_2024/7ain_11799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ain_11799/01_2024/7ain_11799.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ain_11799/01_2024/7ain_11799.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ain_11799/01_2024/7ain_11799_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ain_11799/01_2024/7ain_11799_updated.pdb" } resolution = 3.2 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= 0.002 sd= 0.044 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 4 5.49 5 S 94 5.16 5 C 9020 2.51 5 N 2300 2.21 5 O 2486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 580": "OE1" <-> "OE2" Residue "B GLU 921": "OE1" <-> "OE2" Residue "A PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A GLU 921": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13904 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 6899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 6899 Classifications: {'peptide': 904} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 34, 'TRANS': 869} Chain breaks: 3 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TPO:plan-1': 1, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 6899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 6899 Classifications: {'peptide': 904} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 34, 'TRANS': 869} Chain breaks: 3 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TPO:plan-1': 1, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.64, per 1000 atoms: 0.55 Number of scatterers: 13904 At special positions: 0 Unit cell: (104.811, 92.442, 147.126, 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 94 16.00 P 4 15.00 O 2486 8.00 N 2300 7.00 C 9020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 640 " distance=2.04 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 359 " - pdb=" SG CYS B 369 " distance=2.02 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 640 " distance=2.04 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 359 " - pdb=" SG CYS A 369 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A1101 " - " ASN A 377 " " NAG B1101 " - " ASN B 377 " " NAG C 1 " - " ASN B 328 " " NAG G 1 " - " ASN A 328 " Time building additional restraints: 5.90 Conformation dependent library (CDL) restraints added in 2.5 seconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3332 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 8 sheets defined 55.4% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'B' and resid 112 through 122 Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.676A pdb=" N THR B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Proline residue: B 132 - end of helix No H-bonds generated for 'chain 'B' and resid 127 through 132' Processing helix chain 'B' and resid 136 through 148 removed outlier: 5.151A pdb=" N LEU B 142 " --> pdb=" O MET B 138 " (cutoff:3.500A) Proline residue: B 143 - end of helix Processing helix chain 'B' and resid 152 through 155 No H-bonds generated for 'chain 'B' and resid 152 through 155' Processing helix chain 'B' and resid 157 through 192 removed outlier: 6.234A pdb=" N VAL B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N LEU B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 242 Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 258 through 283 removed outlier: 3.721A pdb=" N VAL B 269 " --> pdb=" O ASN B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 316 removed outlier: 4.756A pdb=" N SER B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE B 316 " --> pdb=" O ILE B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 358 Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 434 through 444 removed outlier: 3.695A pdb=" N GLY B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) Proline residue: B 443 - end of helix Processing helix chain 'B' and resid 448 through 452 Processing helix chain 'B' and resid 461 through 490 Proline residue: B 466 - end of helix removed outlier: 3.672A pdb=" N VAL B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 512 No H-bonds generated for 'chain 'B' and resid 510 through 512' Processing helix chain 'B' and resid 518 through 549 removed outlier: 3.599A pdb=" N PHE B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Proline residue: B 541 - end of helix Processing helix chain 'B' and resid 555 through 560 removed outlier: 3.920A pdb=" N VAL B 558 " --> pdb=" O PHE B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 584 removed outlier: 3.999A pdb=" N LEU B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 615 Proline residue: B 593 - end of helix removed outlier: 3.659A pdb=" N CYS B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 647 Processing helix chain 'B' and resid 649 through 674 removed outlier: 3.603A pdb=" N ILE B 653 " --> pdb=" O TRP B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 695 Processing helix chain 'B' and resid 723 through 733 removed outlier: 3.525A pdb=" N LYS B 733 " --> pdb=" O SER B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 769 Processing helix chain 'B' and resid 784 through 794 removed outlier: 3.938A pdb=" N GLN B 793 " --> pdb=" O SER B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 834 removed outlier: 3.545A pdb=" N PHE B 825 " --> pdb=" O ALA B 821 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 826 " --> pdb=" O TRP B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 847 No H-bonds generated for 'chain 'B' and resid 845 through 847' Processing helix chain 'B' and resid 869 through 880 Proline residue: B 876 - end of helix Processing helix chain 'B' and resid 904 through 916 Processing helix chain 'B' and resid 933 through 945 Processing helix chain 'B' and resid 1029 through 1047 removed outlier: 3.914A pdb=" N LYS B1038 " --> pdb=" O HIS B1034 " (cutoff:3.500A) Processing helix chain 'B' and resid 1064 through 1077 removed outlier: 3.811A pdb=" N ASP B1067 " --> pdb=" O PRO B1064 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU B1068 " --> pdb=" O GLU B1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 122 Processing helix chain 'A' and resid 127 through 132 removed outlier: 3.676A pdb=" N THR A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) Proline residue: A 132 - end of helix No H-bonds generated for 'chain 'A' and resid 127 through 132' Processing helix chain 'A' and resid 136 through 148 removed outlier: 5.151A pdb=" N LEU A 142 " --> pdb=" O MET A 138 " (cutoff:3.500A) Proline residue: A 143 - end of helix Processing helix chain 'A' and resid 152 through 155 No H-bonds generated for 'chain 'A' and resid 152 through 155' Processing helix chain 'A' and resid 157 through 192 removed outlier: 6.234A pdb=" N VAL A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N LEU A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 242 Proline residue: A 211 - end of helix Processing helix chain 'A' and resid 259 through 283 Processing helix chain 'A' and resid 286 through 316 removed outlier: 4.756A pdb=" N SER A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 434 through 444 removed outlier: 3.696A pdb=" N GLY A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 461 through 490 Proline residue: A 466 - end of helix removed outlier: 3.673A pdb=" N VAL A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 518 through 549 removed outlier: 3.599A pdb=" N PHE A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Proline residue: A 541 - end of helix Processing helix chain 'A' and resid 555 through 560 removed outlier: 3.919A pdb=" N VAL A 558 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 584 removed outlier: 3.999A pdb=" N LEU A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 615 Proline residue: A 593 - end of helix removed outlier: 3.659A pdb=" N CYS A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 647 Processing helix chain 'A' and resid 649 through 674 removed outlier: 3.604A pdb=" N ILE A 653 " --> pdb=" O TRP A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 695 Processing helix chain 'A' and resid 723 through 733 removed outlier: 3.524A pdb=" N LYS A 733 " --> pdb=" O SER A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 769 Processing helix chain 'A' and resid 784 through 794 removed outlier: 3.938A pdb=" N GLN A 793 " --> pdb=" O SER A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 834 removed outlier: 3.545A pdb=" N PHE A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 826 " --> pdb=" O TRP A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 847 No H-bonds generated for 'chain 'A' and resid 845 through 847' Processing helix chain 'A' and resid 869 through 880 Proline residue: A 876 - end of helix Processing helix chain 'A' and resid 904 through 916 Processing helix chain 'A' and resid 933 through 945 Processing helix chain 'A' and resid 1029 through 1047 removed outlier: 3.914A pdb=" N LYS A1038 " --> pdb=" O HIS A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1077 removed outlier: 3.811A pdb=" N ASP A1067 " --> pdb=" O PRO A1064 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A1068 " --> pdb=" O GLU A1065 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 322 through 326 Processing sheet with id= B, first strand: chain 'B' and resid 342 through 345 removed outlier: 3.574A pdb=" N VAL B 350 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 1053 through 1056 removed outlier: 3.683A pdb=" N VAL B1084 " --> pdb=" O LYS B 843 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY B 808 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LYS B 713 " --> pdb=" O GLY B 808 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL B 744 " --> pdb=" O LEU B 712 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE B 775 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N SER B 743 " --> pdb=" O PHE B 775 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN B 777 " --> pdb=" O SER B 743 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE B 745 " --> pdb=" O GLN B 777 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B 779 " --> pdb=" O ILE B 745 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 891 through 894 removed outlier: 6.719A pdb=" N GLU B 921 " --> pdb=" O ILE B 892 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR B 894 " --> pdb=" O GLU B 921 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU B 923 " --> pdb=" O THR B 894 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 322 through 326 Processing sheet with id= F, first strand: chain 'A' and resid 342 through 345 removed outlier: 3.575A pdb=" N VAL A 350 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1053 through 1056 removed outlier: 3.683A pdb=" N VAL A1084 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY A 808 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LYS A 713 " --> pdb=" O GLY A 808 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL A 744 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE A 775 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N SER A 743 " --> pdb=" O PHE A 775 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN A 777 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE A 745 " --> pdb=" O GLN A 777 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A 779 " --> pdb=" O ILE A 745 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 891 through 894 removed outlier: 6.718A pdb=" N GLU A 921 " --> pdb=" O ILE A 892 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR A 894 " --> pdb=" O GLU A 921 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU A 923 " --> pdb=" O THR A 894 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 723 hydrogen bonds defined for protein. 1983 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: 4.63 Time building geometry restraints manager: 6.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4376 1.35 - 1.47: 3663 1.47 - 1.60: 6015 1.60 - 1.73: 14 1.73 - 1.86: 150 Bond restraints: 14218 Sorted by residual: bond pdb=" OG1 TPO B 727 " pdb=" P TPO B 727 " ideal model delta sigma weight residual 1.717 1.617 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" OG1 TPO A 727 " pdb=" P TPO A 727 " ideal model delta sigma weight residual 1.717 1.617 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" O1P TPO A 727 " pdb=" P TPO A 727 " ideal model delta sigma weight residual 1.525 1.614 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" O1P TPO B 727 " pdb=" P TPO B 727 " ideal model delta sigma weight residual 1.525 1.614 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" O2P TPO A 727 " pdb=" P TPO A 727 " ideal model delta sigma weight residual 1.528 1.605 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 14213 not shown) Histogram of bond angle deviations from ideal: 97.39 - 104.75: 245 104.75 - 112.11: 7431 112.11 - 119.47: 4656 119.47 - 126.84: 6801 126.84 - 134.20: 209 Bond angle restraints: 19342 Sorted by residual: angle pdb=" C VAL B 866 " pdb=" N HIS B 867 " pdb=" CA HIS B 867 " ideal model delta sigma weight residual 122.53 115.85 6.68 1.61e+00 3.86e-01 1.72e+01 angle pdb=" C VAL A 866 " pdb=" N HIS A 867 " pdb=" CA HIS A 867 " ideal model delta sigma weight residual 122.53 115.88 6.65 1.61e+00 3.86e-01 1.71e+01 angle pdb=" CA CYS B 640 " pdb=" CB CYS B 640 " pdb=" SG CYS B 640 " ideal model delta sigma weight residual 114.40 122.59 -8.19 2.30e+00 1.89e-01 1.27e+01 angle pdb=" CA CYS A 640 " pdb=" CB CYS A 640 " pdb=" SG CYS A 640 " ideal model delta sigma weight residual 114.40 122.58 -8.18 2.30e+00 1.89e-01 1.27e+01 angle pdb=" C ASP A 255 " pdb=" CA ASP A 255 " pdb=" CB ASP A 255 " ideal model delta sigma weight residual 116.63 112.53 4.10 1.16e+00 7.43e-01 1.25e+01 ... (remaining 19337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.88: 7986 20.88 - 41.76: 354 41.76 - 62.64: 68 62.64 - 83.52: 22 83.52 - 104.39: 8 Dihedral angle restraints: 8438 sinusoidal: 3256 harmonic: 5182 Sorted by residual: dihedral pdb=" CA CYS B 640 " pdb=" C CYS B 640 " pdb=" N LEU B 641 " pdb=" CA LEU B 641 " ideal model delta harmonic sigma weight residual 180.00 155.75 24.25 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA CYS A 640 " pdb=" C CYS A 640 " pdb=" N LEU A 641 " pdb=" CA LEU A 641 " ideal model delta harmonic sigma weight residual 180.00 155.76 24.24 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CB CYS A 179 " pdb=" SG CYS A 179 " pdb=" SG CYS A 640 " pdb=" CB CYS A 640 " ideal model delta sinusoidal sigma weight residual 93.00 60.81 32.19 1 1.00e+01 1.00e-02 1.48e+01 ... (remaining 8435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1924 0.079 - 0.157: 345 0.157 - 0.236: 15 0.236 - 0.314: 2 0.314 - 0.393: 2 Chirality restraints: 2288 Sorted by residual: chirality pdb=" CA CYS B 640 " pdb=" N CYS B 640 " pdb=" C CYS B 640 " pdb=" CB CYS B 640 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA CYS A 640 " pdb=" N CYS A 640 " pdb=" C CYS A 640 " pdb=" CB CYS A 640 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 2285 not shown) Planarity restraints: 2404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 497 " -0.094 9.50e-02 1.11e+02 5.58e-02 1.77e+01 pdb=" NE ARG B 497 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 497 " -0.069 2.00e-02 2.50e+03 pdb=" NH1 ARG B 497 " 0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG B 497 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 497 " 0.093 9.50e-02 1.11e+02 5.54e-02 1.76e+01 pdb=" NE ARG A 497 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 497 " 0.069 2.00e-02 2.50e+03 pdb=" NH1 ARG A 497 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG A 497 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 240 " 0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C PHE A 240 " -0.070 2.00e-02 2.50e+03 pdb=" O PHE A 240 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU A 241 " 0.024 2.00e-02 2.50e+03 ... (remaining 2401 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 4023 2.81 - 3.33: 14364 3.33 - 3.85: 23473 3.85 - 4.38: 27239 4.38 - 4.90: 46654 Nonbonded interactions: 115753 Sorted by model distance: nonbonded pdb=" OH TYR B 141 " pdb=" OG1 THR B 475 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR A 141 " pdb=" OG1 THR A 475 " model vdw 2.282 2.440 nonbonded pdb=" O SER B1092 " pdb=" OG SER B1092 " model vdw 2.291 2.440 nonbonded pdb=" ND2 ASN B1040 " pdb=" O VAL B1076 " model vdw 2.291 2.520 nonbonded pdb=" ND2 ASN A1040 " pdb=" O VAL A1076 " model vdw 2.292 2.520 ... (remaining 115748 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.970 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: 13.840 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 38.980 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 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 : 0.011 0.100 14218 Z= 0.693 Angle : 0.927 11.687 19342 Z= 0.500 Chirality : 0.057 0.393 2288 Planarity : 0.006 0.065 2400 Dihedral : 13.500 104.395 5088 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.81 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.18), residues: 1780 helix: -0.37 (0.15), residues: 980 sheet: -1.64 (0.47), residues: 78 loop : -1.81 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 809 HIS 0.013 0.001 HIS A 790 PHE 0.034 0.003 PHE A 877 TYR 0.018 0.002 TYR A 663 ARG 0.071 0.002 ARG B 497 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.471 Fit side-chains REVERT: B 397 TRP cc_start: 0.7722 (m100) cc_final: 0.7509 (m100) REVERT: B 459 LYS cc_start: 0.8010 (mttt) cc_final: 0.7784 (mttp) REVERT: B 597 MET cc_start: 0.7873 (tpp) cc_final: 0.7636 (tpp) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.2970 time to fit residues: 132.7240 Evaluate side-chains 181 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.0170 chunk 136 optimal weight: 0.0870 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 0.0970 chunk 92 optimal weight: 8.9990 chunk 72 optimal weight: 0.6980 chunk 141 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 0.0270 chunk 105 optimal weight: 20.0000 chunk 163 optimal weight: 0.9980 overall best weight: 0.1852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 629 HIS B 703 ASN B 752 ASN B 854 GLN B 882 HIS B1040 ASN A 133 GLN A 629 HIS A 752 ASN A 882 HIS A1040 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14218 Z= 0.190 Angle : 0.613 10.699 19342 Z= 0.307 Chirality : 0.042 0.237 2288 Planarity : 0.005 0.045 2400 Dihedral : 6.903 78.831 2088 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.64 % Favored : 97.25 % Rotamer: Outliers : 2.15 % Allowed : 11.43 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.19), residues: 1780 helix: 0.61 (0.16), residues: 996 sheet: -1.20 (0.50), residues: 78 loop : -1.48 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 649 HIS 0.005 0.001 HIS A 867 PHE 0.028 0.002 PHE A 877 TYR 0.030 0.002 TYR B 937 ARG 0.014 0.001 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 220 time to evaluate : 1.466 Fit side-chains revert: symmetry clash REVERT: A 597 MET cc_start: 0.7267 (tpp) cc_final: 0.6956 (tpp) REVERT: A 915 HIS cc_start: 0.5513 (t-90) cc_final: 0.5291 (t-170) REVERT: A 1070 TYR cc_start: 0.8708 (t80) cc_final: 0.8399 (t80) outliers start: 31 outliers final: 11 residues processed: 242 average time/residue: 0.2393 time to fit residues: 86.9168 Evaluate side-chains 187 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 176 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1087 VAL Chi-restraints excluded: chain B residue 1093 GLU Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 565 ASN Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 887 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 53.0256 > 50: distance: 73 - 77: 12.698 distance: 77 - 78: 5.476 distance: 78 - 79: 9.871 distance: 78 - 81: 11.802 distance: 79 - 80: 20.045 distance: 79 - 86: 10.305 distance: 81 - 82: 7.657 distance: 82 - 83: 9.206 distance: 83 - 84: 5.860 distance: 84 - 85: 9.013 distance: 86 - 87: 23.281 distance: 87 - 88: 13.673 distance: 87 - 90: 21.340 distance: 88 - 89: 16.632 distance: 88 - 91: 24.038 distance: 91 - 92: 14.188 distance: 92 - 93: 30.727 distance: 92 - 95: 39.217 distance: 93 - 94: 30.669 distance: 93 - 99: 17.201 distance: 95 - 96: 8.598 distance: 96 - 97: 19.282 distance: 96 - 98: 16.089 distance: 99 - 100: 14.828 distance: 100 - 101: 26.266 distance: 101 - 102: 8.299 distance: 101 - 103: 24.584 distance: 103 - 104: 26.281 distance: 104 - 105: 17.603 distance: 104 - 107: 27.352 distance: 105 - 106: 11.310 distance: 105 - 112: 10.085 distance: 107 - 108: 28.021 distance: 108 - 109: 22.243 distance: 109 - 110: 20.274 distance: 109 - 111: 17.311 distance: 112 - 113: 4.214 distance: 112 - 118: 8.228 distance: 113 - 114: 9.508 distance: 113 - 116: 9.334 distance: 114 - 115: 17.134 distance: 114 - 119: 21.754 distance: 116 - 117: 11.383 distance: 117 - 118: 12.103 distance: 119 - 120: 4.546 distance: 120 - 121: 9.265 distance: 120 - 123: 6.579 distance: 121 - 122: 28.180 distance: 121 - 126: 11.499 distance: 123 - 124: 12.754 distance: 123 - 125: 17.477 distance: 126 - 127: 13.446 distance: 127 - 128: 5.765 distance: 127 - 130: 10.512 distance: 128 - 129: 4.349 distance: 128 - 140: 13.409 distance: 130 - 131: 4.193 distance: 132 - 134: 3.439 distance: 133 - 135: 3.738 distance: 133 - 136: 3.686 distance: 134 - 135: 3.461 distance: 135 - 137: 3.870 distance: 136 - 138: 3.712 distance: 138 - 139: 3.508 distance: 140 - 141: 7.644 distance: 141 - 142: 10.754 distance: 141 - 144: 13.326 distance: 142 - 143: 10.514 distance: 142 - 145: 16.952 distance: 143 - 165: 25.212 distance: 145 - 146: 7.584 distance: 146 - 147: 4.738 distance: 146 - 149: 10.008 distance: 147 - 148: 7.938 distance: 147 - 153: 7.476 distance: 148 - 172: 11.281 distance: 149 - 150: 14.787 distance: 150 - 151: 4.010 distance: 150 - 152: 8.699