Starting phenix.real_space_refine on Thu Aug 8 16:11:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4r_28857/08_2024/8f4r_28857.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4r_28857/08_2024/8f4r_28857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4r_28857/08_2024/8f4r_28857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4r_28857/08_2024/8f4r_28857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4r_28857/08_2024/8f4r_28857.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4r_28857/08_2024/8f4r_28857.cif" } resolution = 3.06 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= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 15122 2.51 5 N 3992 2.21 5 O 4429 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 23675 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7865 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 989} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 7898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 7898 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 991} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 7881 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 991} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'LLL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.10, per 1000 atoms: 0.55 Number of scatterers: 23675 At special positions: 0 Unit cell: (124.12, 114.49, 141.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 4429 8.00 N 3992 7.00 C 15122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.90 Conformation dependent library (CDL) restraints added in 4.2 seconds 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5708 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 25 sheets defined 59.7% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 3.516A pdb=" N PHE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 7 " --> pdb=" O ASN A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 30 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 69 removed outlier: 3.523A pdb=" N ASN A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.962A pdb=" N SER A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.630A pdb=" N PHE A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 329 through 359 Processing helix chain 'A' and resid 361 through 386 Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 424 removed outlier: 4.160A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 437 Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 460 through 497 removed outlier: 4.554A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix removed outlier: 3.774A pdb=" N LEU A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 510 through 536 Processing helix chain 'A' and resid 536 through 558 removed outlier: 3.863A pdb=" N TRP A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 601 Processing helix chain 'A' and resid 642 through 656 Processing helix chain 'A' and resid 690 through 708 removed outlier: 3.683A pdb=" N GLU A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'A' and resid 740 through 752 Processing helix chain 'A' and resid 775 through 778 Processing helix chain 'A' and resid 780 through 786 Processing helix chain 'A' and resid 799 through 802 No H-bonds generated for 'chain 'A' and resid 799 through 802' Processing helix chain 'A' and resid 834 through 849 Processing helix chain 'A' and resid 859 through 867 Processing helix chain 'A' and resid 869 through 891 removed outlier: 3.712A pdb=" N ALA A 873 " --> pdb=" O ALA A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.830A pdb=" N VAL A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 917 removed outlier: 3.631A pdb=" N GLY A 906 " --> pdb=" O VAL A 902 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 907 " --> pdb=" O VAL A 903 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 910 " --> pdb=" O GLY A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 953 Processing helix chain 'A' and resid 956 through 988 removed outlier: 4.549A pdb=" N ARG A 970 " --> pdb=" O ARG A 966 " (cutoff:3.500A) Proline residue: A 971 - end of helix Proline residue: A 985 - end of helix Processing helix chain 'A' and resid 993 through 1030 removed outlier: 4.271A pdb=" N TYR A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Proline residue: A1020 - end of helix Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.775A pdb=" N ASP B 7 " --> pdb=" O ASN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 28 removed outlier: 3.634A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 28 " --> pdb=" O THR B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 70 removed outlier: 4.056A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET B 69 " --> pdb=" O ILE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 112 removed outlier: 3.627A pdb=" N GLN B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.523A pdb=" N PHE B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 315 removed outlier: 3.702A pdb=" N GLN B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 359 Processing helix chain 'B' and resid 361 through 386 removed outlier: 3.747A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix removed outlier: 3.662A pdb=" N VAL B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 424 removed outlier: 3.507A pdb=" N ILE B 402 " --> pdb=" O MET B 398 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 452 removed outlier: 3.917A pdb=" N GLY B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 459 removed outlier: 4.637A pdb=" N MET B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 452 through 459' Processing helix chain 'B' and resid 460 through 486 Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.991A pdb=" N ALA B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 535 removed outlier: 4.668A pdb=" N ASN B 516 " --> pdb=" O PHE B 512 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS B 535 " --> pdb=" O ALA B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 556 removed outlier: 4.077A pdb=" N TRP B 540 " --> pdb=" O ARG B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 600 Processing helix chain 'B' and resid 642 through 655 Processing helix chain 'B' and resid 690 through 708 Processing helix chain 'B' and resid 730 through 738 Processing helix chain 'B' and resid 740 through 753 Processing helix chain 'B' and resid 775 through 778 Processing helix chain 'B' and resid 780 through 786 removed outlier: 3.683A pdb=" N ILE B 784 " --> pdb=" O PRO B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 847 removed outlier: 3.571A pdb=" N LYS B 847 " --> pdb=" O GLU B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 891 Proline residue: B 872 - end of helix Processing helix chain 'B' and resid 894 through 901 Processing helix chain 'B' and resid 902 through 918 removed outlier: 3.602A pdb=" N GLY B 906 " --> pdb=" O VAL B 902 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY B 909 " --> pdb=" O LEU B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 954 removed outlier: 4.564A pdb=" N PHE B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 968 Processing helix chain 'B' and resid 968 through 988 removed outlier: 3.588A pdb=" N ILE B 972 " --> pdb=" O ARG B 968 " (cutoff:3.500A) Proline residue: B 985 - end of helix Processing helix chain 'B' and resid 993 through 1014 removed outlier: 3.717A pdb=" N GLN B 997 " --> pdb=" O GLY B 993 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY B1003 " --> pdb=" O ALA B 999 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL B1004 " --> pdb=" O VAL B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1030 Proline residue: B1020 - end of helix Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 8 through 30 removed outlier: 3.559A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 69 removed outlier: 3.527A pdb=" N ASN C 68 " --> pdb=" O VAL C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 removed outlier: 4.139A pdb=" N SER C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA C 114 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.766A pdb=" N VAL C 203 " --> pdb=" O THR C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.545A pdb=" N PHE C 246 " --> pdb=" O THR C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 315 Processing helix chain 'C' and resid 329 through 360 removed outlier: 3.622A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 387 removed outlier: 3.843A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 3.569A pdb=" N ALA C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 391 through 401 Processing helix chain 'C' and resid 401 through 423 removed outlier: 4.176A pdb=" N ASP C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 459 removed outlier: 5.757A pdb=" N GLY C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL C 443 " --> pdb=" O GLN C 439 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Proline residue: C 455 - end of helix removed outlier: 3.988A pdb=" N PHE C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE C 459 " --> pdb=" O PRO C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 496 removed outlier: 4.593A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 511 through 532 Processing helix chain 'C' and resid 536 through 558 removed outlier: 4.484A pdb=" N TRP C 540 " --> pdb=" O ARG C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 600 Processing helix chain 'C' and resid 642 through 657 Processing helix chain 'C' and resid 690 through 708 Processing helix chain 'C' and resid 730 through 737 Processing helix chain 'C' and resid 740 through 752 Processing helix chain 'C' and resid 775 through 778 Processing helix chain 'C' and resid 780 through 786 Processing helix chain 'C' and resid 834 through 849 Processing helix chain 'C' and resid 859 through 867 Processing helix chain 'C' and resid 870 through 891 Processing helix chain 'C' and resid 894 through 901 Processing helix chain 'C' and resid 902 through 917 removed outlier: 3.998A pdb=" N GLY C 909 " --> pdb=" O LEU C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 954 removed outlier: 3.752A pdb=" N ILE C 943 " --> pdb=" O ASN C 939 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 988 removed outlier: 4.867A pdb=" N ARG C 970 " --> pdb=" O ARG C 966 " (cutoff:3.500A) Proline residue: C 971 - end of helix Proline residue: C 985 - end of helix Processing helix chain 'C' and resid 993 through 1030 removed outlier: 4.314A pdb=" N GLY C1003 " --> pdb=" O ALA C 999 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE C1016 " --> pdb=" O THR C1012 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TYR C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Proline residue: C1020 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 132 removed outlier: 4.718A pdb=" N ASN A 42 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 77 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 12.701A pdb=" N ARG A 813 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N GLU A 824 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU A 815 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU A 824 " --> pdb=" O HIS A 716 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N HIS A 716 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 826 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL A 714 " --> pdb=" O VAL A 826 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 132 removed outlier: 4.718A pdb=" N ASN A 42 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 77 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 12.701A pdb=" N ARG A 813 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N GLU A 824 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU A 815 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N SER A 821 " --> pdb=" O ASP A 685 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASP A 680 " --> pdb=" O THR A 858 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.989A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 138 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU A 293 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ASN A 136 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILE A 137 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU A 328 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N THR A 139 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.989A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL A 623 " --> pdb=" O GLY A 613 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N GLY A 615 " --> pdb=" O GLN A 621 " (cutoff:3.500A) removed outlier: 9.637A pdb=" N GLN A 621 " --> pdb=" O GLY A 615 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.364A pdb=" N TYR A 182 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS A 768 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN A 758 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL A 771 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TYR A 756 " --> pdb=" O VAL A 771 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 215 through 218 removed outlier: 3.508A pdb=" N GLY A 217 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR A 233 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE B 727 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN A 235 " --> pdb=" O ILE B 727 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE B 729 " --> pdb=" O ASN A 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 253 Processing sheet with id=AA8, first strand: chain 'A' and resid 803 through 810 removed outlier: 8.563A pdb=" N ASN C 235 " --> pdb=" O PRO A 723 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 725 " --> pdb=" O ASN C 235 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY C 217 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB1, first strand: chain 'B' and resid 75 through 80 removed outlier: 6.984A pdb=" N SER B 93 " --> pdb=" O MET B 76 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N MET B 78 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR B 91 " --> pdb=" O MET B 78 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER B 80 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N SER B 89 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 172 through 177 removed outlier: 4.835A pdb=" N SER B 144 " --> pdb=" O PRO B 285 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 138 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU B 293 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN B 136 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ILE B 137 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLU B 328 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THR B 139 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 4.251A pdb=" N SER B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 266 through 272 removed outlier: 8.386A pdb=" N TYR B 182 " --> pdb=" O VAL B 766 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS B 768 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN B 758 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL B 771 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N TYR B 756 " --> pdb=" O VAL B 771 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 218 through 219 removed outlier: 4.717A pdb=" N THR B 233 " --> pdb=" O PRO C 723 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.841A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 711 through 716 removed outlier: 4.995A pdb=" N ARG B 713 " --> pdb=" O GLU B 828 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU B 828 " --> pdb=" O ARG B 713 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 711 through 716 removed outlier: 4.995A pdb=" N ARG B 713 " --> pdb=" O GLU B 828 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU B 828 " --> pdb=" O ARG B 713 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N SER B 821 " --> pdb=" O ASP B 685 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 788 through 790 Processing sheet with id=AC1, first strand: chain 'C' and resid 128 through 130 removed outlier: 4.024A pdb=" N GLN C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) removed outlier: 12.333A pdb=" N ARG C 813 " --> pdb=" O GLU C 824 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N GLU C 824 " --> pdb=" O ARG C 813 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU C 815 " --> pdb=" O ALA C 822 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU C 828 " --> pdb=" O ARG C 713 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ARG C 713 " --> pdb=" O GLU C 828 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 128 through 130 removed outlier: 4.024A pdb=" N GLN C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) removed outlier: 12.333A pdb=" N ARG C 813 " --> pdb=" O GLU C 824 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N GLU C 824 " --> pdb=" O ARG C 813 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU C 815 " --> pdb=" O ALA C 822 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.658A pdb=" N SER C 144 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU C 138 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR C 139 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.290A pdb=" N SER C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.798A pdb=" N TYR C 182 " --> pdb=" O VAL C 766 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS C 768 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN C 758 " --> pdb=" O VAL C 769 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL C 771 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N TYR C 756 " --> pdb=" O VAL C 771 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 250 through 253 removed outlier: 6.657A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 788 through 790 1625 hydrogen bonds defined for protein. 4758 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: 11.37 Time building geometry restraints manager: 9.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7775 1.34 - 1.46: 3862 1.46 - 1.57: 12240 1.57 - 1.69: 5 1.69 - 1.81: 252 Bond restraints: 24134 Sorted by residual: bond pdb=" C51 LLL B1101 " pdb=" C61 LLL B1101 " ideal model delta sigma weight residual 1.515 1.590 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C42 LLL B1101 " pdb=" C52 LLL B1101 " ideal model delta sigma weight residual 1.529 1.601 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" CA PHE A1030 " pdb=" C PHE A1030 " ideal model delta sigma weight residual 1.532 1.511 0.022 6.50e-03 2.37e+04 1.10e+01 bond pdb=" C32 LLL B1101 " pdb=" C42 LLL B1101 " ideal model delta sigma weight residual 1.529 1.592 -0.063 2.00e-02 2.50e+03 9.93e+00 bond pdb=" C33 LLL B1101 " pdb=" C43 LLL B1101 " ideal model delta sigma weight residual 1.541 1.603 -0.062 2.00e-02 2.50e+03 9.61e+00 ... (remaining 24129 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.65: 690 106.65 - 113.49: 13429 113.49 - 120.33: 8414 120.33 - 127.17: 10049 127.17 - 134.00: 218 Bond angle restraints: 32800 Sorted by residual: angle pdb=" C ALA B 859 " pdb=" CA ALA B 859 " pdb=" CB ALA B 859 " ideal model delta sigma weight residual 116.54 110.06 6.48 1.15e+00 7.56e-01 3.18e+01 angle pdb=" C LEU B 500 " pdb=" CA LEU B 500 " pdb=" CB LEU B 500 " ideal model delta sigma weight residual 117.23 110.78 6.45 1.36e+00 5.41e-01 2.25e+01 angle pdb=" C ASN C 818 " pdb=" CA ASN C 818 " pdb=" CB ASN C 818 " ideal model delta sigma weight residual 116.54 111.21 5.33 1.15e+00 7.56e-01 2.15e+01 angle pdb=" C SER C 894 " pdb=" N VAL C 895 " pdb=" CA VAL C 895 " ideal model delta sigma weight residual 120.24 122.84 -2.60 6.30e-01 2.52e+00 1.70e+01 angle pdb=" CA ALA B 859 " pdb=" C ALA B 859 " pdb=" N MET B 860 " ideal model delta sigma weight residual 119.52 116.45 3.07 7.90e-01 1.60e+00 1.51e+01 ... (remaining 32795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.83: 14095 25.83 - 51.66: 301 51.66 - 77.48: 35 77.48 - 103.31: 7 103.31 - 129.14: 8 Dihedral angle restraints: 14446 sinusoidal: 5554 harmonic: 8892 Sorted by residual: dihedral pdb=" O23 LLL B1101 " pdb=" C13 LLL B1101 " pdb=" C23 LLL B1101 " pdb=" O53 LLL B1101 " ideal model delta sinusoidal sigma weight residual 178.81 -52.05 -129.14 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C11 LLL B1101 " pdb=" C51 LLL B1101 " pdb=" O51 LLL B1101 " pdb=" C61 LLL B1101 " ideal model delta sinusoidal sigma weight residual 174.24 -57.43 -128.33 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C11 LLL B1101 " pdb=" C51 LLL B1101 " pdb=" O51 LLL B1101 " pdb=" C41 LLL B1101 " ideal model delta sinusoidal sigma weight residual -60.30 64.56 -124.86 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 14443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 3811 0.134 - 0.269: 5 0.269 - 0.403: 4 0.403 - 0.537: 1 0.537 - 0.671: 3 Chirality restraints: 3824 Sorted by residual: chirality pdb=" C62 LLL B1101 " pdb=" C12 LLL B1101 " pdb=" C52 LLL B1101 " pdb=" O62 LLL B1101 " both_signs ideal model delta sigma weight residual False -2.49 -3.16 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C42 LLL B1101 " pdb=" C32 LLL B1101 " pdb=" C52 LLL B1101 " pdb=" O11 LLL B1101 " both_signs ideal model delta sigma weight residual False 2.54 3.21 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" C52 LLL B1101 " pdb=" C42 LLL B1101 " pdb=" C62 LLL B1101 " pdb=" O52 LLL B1101 " both_signs ideal model delta sigma weight residual False -2.47 -3.05 0.58 2.00e-01 2.50e+01 8.38e+00 ... (remaining 3821 not shown) Planarity restraints: 4225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 871 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO C 872 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 872 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 872 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 426 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO A 427 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 427 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 427 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 830 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO B 831 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 831 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 831 " -0.017 5.00e-02 4.00e+02 ... (remaining 4222 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3446 2.75 - 3.29: 24065 3.29 - 3.82: 40546 3.82 - 4.36: 47331 4.36 - 4.90: 83583 Nonbonded interactions: 198971 Sorted by model distance: nonbonded pdb=" O ALA A 451 " pdb=" OG SER A 878 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR A 526 " pdb=" O ILE A1016 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 759 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR C 526 " pdb=" O ILE C1016 " model vdw 2.232 3.040 nonbonded pdb=" OD1 ASP B 153 " pdb=" OH TYR B 182 " model vdw 2.276 3.040 ... (remaining 198966 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 94 or (resid 95 through 96 and (name N or name C \ A or name C or name O or name CB )) or resid 97 through 432 or (resid 433 and (n \ ame N or name CA or name C or name O or name CB )) or resid 434 through 505 or ( \ resid 506 and (name N or name CA or name C or name O or name CB )) or (resid 507 \ through 509 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 10 through 1031)) selection = (chain 'B' and (resid 1 through 94 or (resid 95 through 96 and (name N or name C \ A or name C or name O or name CB )) or resid 97 through 432 or (resid 433 and (n \ ame N or name CA or name C or name O or name CB )) or resid 434 through 499 or ( \ resid 500 through 502 and (name N or name CA or name C or name O or name CB )) o \ r (resid 503 through 506 and (name N or name CA or name C or name O or name CB ) \ ) or resid 507 or (resid 508 through 509 and (name N or name CA or name C or nam \ e O or name CB )) or resid 510 through 638 or (resid 639 and (name N or name CA \ or name C or name O or name CB )) or resid 640 through 657 or (resid 658 and (na \ me N or name CA or name C or name O or name CB )) or resid 659 through 1031)) selection = (chain 'C' and (resid 1 through 499 or (resid 500 through 502 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 503 through 506 and (name N or \ name CA or name C or name O or name CB )) or resid 507 or (resid 508 through 509 \ and (name N or name CA or name C or name O or name CB )) or resid 510 through 6 \ 57 or (resid 658 and (name N or name CA or name C or name O or name CB )) or res \ id 659 through 1031)) } 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: 4.390 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: 0.870 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 65.900 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 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 : 0.004 0.075 24134 Z= 0.282 Angle : 0.561 10.117 32800 Z= 0.324 Chirality : 0.044 0.671 3824 Planarity : 0.003 0.038 4225 Dihedral : 11.500 129.138 8738 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.23 % Favored : 98.74 % Rotamer: Outliers : 3.22 % Allowed : 5.53 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.85 (0.15), residues: 3091 helix: 2.32 (0.12), residues: 1691 sheet: -0.26 (0.26), residues: 427 loop : 0.04 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 540 HIS 0.005 0.001 HIS A 506 PHE 0.010 0.001 PHE C 571 TYR 0.010 0.001 TYR C 862 ARG 0.005 0.000 ARG B 813 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 640 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 ASN cc_start: 0.7791 (m110) cc_final: 0.7572 (m110) REVERT: A 799 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8421 (t80) REVERT: B 135 THR cc_start: 0.7241 (p) cc_final: 0.6754 (p) REVERT: B 682 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7134 (tp30) REVERT: B 726 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7497 (tp40) REVERT: B 880 LEU cc_start: 0.8478 (tp) cc_final: 0.8232 (tp) REVERT: C 270 MET cc_start: 0.8061 (ttp) cc_final: 0.7677 (ttp) REVERT: C 683 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8233 (tp) REVERT: C 731 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.6050 (mp10) REVERT: C 777 TYR cc_start: 0.8573 (m-80) cc_final: 0.8260 (m-80) outliers start: 81 outliers final: 25 residues processed: 696 average time/residue: 0.3481 time to fit residues: 381.9064 Evaluate side-chains 420 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 390 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 726 GLN Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 683 LEU Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 731 GLN Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 833 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 4.9990 chunk 234 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 147 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 chunk 280 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 59 ASN A 81 GLN A 87 GLN A 105 GLN A 108 GLN A 124 ASN A 163 GLN A 213 GLN A 237 GLN A 437 GLN A 439 GLN A 469 GLN A 517 GLN A 583 GLN A 585 GLN A 592 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 GLN A 921 ASN A 926 GLN B 109 ASN B 163 GLN B 213 GLN B 255 GLN B 592 GLN B 700 GLN B 708 ASN B 716 HIS B 724 GLN B 726 GLN B 749 GLN B 818 ASN B 926 GLN B 951 ASN C 87 GLN C 110 GLN C 123 GLN C 194 ASN C 241 GLN C 254 ASN ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 GLN C 655 ASN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 HIS C 700 GLN C 716 HIS C 735 GLN C 745 ASN C 749 GLN C 863 GLN C 967 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24134 Z= 0.258 Angle : 0.561 9.330 32800 Z= 0.291 Chirality : 0.041 0.259 3824 Planarity : 0.004 0.042 4225 Dihedral : 8.097 105.793 3443 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.16 % Favored : 98.80 % Rotamer: Outliers : 3.90 % Allowed : 9.23 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.84 (0.15), residues: 3091 helix: 2.33 (0.12), residues: 1714 sheet: -0.31 (0.25), residues: 438 loop : -0.03 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 540 HIS 0.008 0.001 HIS A 506 PHE 0.023 0.001 PHE C 511 TYR 0.014 0.001 TYR B 467 ARG 0.006 0.000 ARG B 813 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 424 time to evaluate : 2.385 Fit side-chains revert: symmetry clash REVERT: A 799 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.8373 (t80) REVERT: B 135 THR cc_start: 0.7176 (p) cc_final: 0.6779 (p) REVERT: B 168 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.6777 (mpp-170) REVERT: B 682 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7158 (tp30) REVERT: B 880 LEU cc_start: 0.8434 (tp) cc_final: 0.8219 (tp) REVERT: C 731 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6020 (mp10) REVERT: C 777 TYR cc_start: 0.8545 (m-80) cc_final: 0.8233 (m-80) outliers start: 98 outliers final: 51 residues processed: 493 average time/residue: 0.3262 time to fit residues: 256.3819 Evaluate side-chains 413 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 358 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 731 GLN Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 932 VAL Chi-restraints excluded: chain C residue 944 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 233 optimal weight: 0.8980 chunk 191 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 281 optimal weight: 4.9990 chunk 303 optimal weight: 0.9990 chunk 250 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 GLN A 517 GLN A 921 ASN ** A 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN B 745 ASN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 HIS C 951 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24134 Z= 0.228 Angle : 0.536 10.100 32800 Z= 0.274 Chirality : 0.040 0.266 3824 Planarity : 0.004 0.045 4225 Dihedral : 6.964 88.248 3424 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.10 % Favored : 98.87 % Rotamer: Outliers : 4.02 % Allowed : 10.94 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.75 (0.15), residues: 3091 helix: 2.26 (0.12), residues: 1716 sheet: -0.33 (0.25), residues: 417 loop : -0.12 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 540 HIS 0.007 0.001 HIS A 506 PHE 0.019 0.001 PHE C 511 TYR 0.012 0.001 TYR C 526 ARG 0.004 0.000 ARG C1028 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 388 time to evaluate : 2.591 Fit side-chains revert: symmetry clash REVERT: A 799 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8363 (t80) REVERT: B 135 THR cc_start: 0.7102 (p) cc_final: 0.6706 (p) REVERT: B 168 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.6696 (mtp180) REVERT: C 731 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.6043 (mp10) REVERT: C 777 TYR cc_start: 0.8470 (m-80) cc_final: 0.8107 (m-80) outliers start: 101 outliers final: 63 residues processed: 456 average time/residue: 0.3394 time to fit residues: 248.6960 Evaluate side-chains 412 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 346 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 731 GLN Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 932 VAL Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 1009 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 282 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 267 optimal weight: 0.0060 chunk 80 optimal weight: 3.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS A 439 GLN A 517 GLN ** A 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 GLN B 951 ASN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24134 Z= 0.256 Angle : 0.534 9.744 32800 Z= 0.273 Chirality : 0.040 0.325 3824 Planarity : 0.003 0.045 4225 Dihedral : 6.214 73.438 3421 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.16 % Favored : 98.80 % Rotamer: Outliers : 4.46 % Allowed : 11.34 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.70 (0.15), residues: 3091 helix: 2.22 (0.12), residues: 1717 sheet: -0.36 (0.25), residues: 429 loop : -0.14 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 540 HIS 0.007 0.001 HIS A 506 PHE 0.016 0.001 PHE C 511 TYR 0.012 0.001 TYR C 327 ARG 0.004 0.000 ARG C1027 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 374 time to evaluate : 3.048 Fit side-chains revert: symmetry clash REVERT: A 799 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8428 (t80) REVERT: B 135 THR cc_start: 0.7148 (p) cc_final: 0.6774 (p) REVERT: B 168 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.6628 (mtp180) REVERT: C 270 MET cc_start: 0.8054 (ttm) cc_final: 0.7649 (tpp) REVERT: C 731 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.6026 (mp10) REVERT: C 777 TYR cc_start: 0.8534 (m-80) cc_final: 0.8190 (m-80) outliers start: 112 outliers final: 74 residues processed: 443 average time/residue: 0.3300 time to fit residues: 235.4708 Evaluate side-chains 426 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 349 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 731 GLN Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 892 SER Chi-restraints excluded: chain C residue 932 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1009 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 123 optimal weight: 0.5980 chunk 254 optimal weight: 4.9990 chunk 206 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 268 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN B 3 ASN B 254 ASN B 684 GLN B 686 HIS ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24134 Z= 0.278 Angle : 0.537 9.867 32800 Z= 0.275 Chirality : 0.041 0.323 3824 Planarity : 0.004 0.045 4225 Dihedral : 5.870 60.885 3419 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.16 % Favored : 98.80 % Rotamer: Outliers : 4.30 % Allowed : 12.10 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.65 (0.15), residues: 3091 helix: 2.16 (0.12), residues: 1719 sheet: -0.30 (0.26), residues: 403 loop : -0.17 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 540 HIS 0.007 0.001 HIS A 506 PHE 0.015 0.001 PHE A 352 TYR 0.012 0.001 TYR A 890 ARG 0.003 0.000 ARG B 813 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 363 time to evaluate : 2.650 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.8267 (mtp) cc_final: 0.8014 (mtt) REVERT: A 182 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: A 799 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8397 (t80) REVERT: B 135 THR cc_start: 0.7211 (p) cc_final: 0.6827 (p) REVERT: B 168 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.6654 (mtp180) REVERT: C 731 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.6065 (mp10) REVERT: C 777 TYR cc_start: 0.8516 (m-80) cc_final: 0.8215 (m-80) outliers start: 108 outliers final: 71 residues processed: 431 average time/residue: 0.3296 time to fit residues: 230.5504 Evaluate side-chains 422 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 347 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 731 GLN Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 932 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1009 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 5.9990 chunk 268 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 175 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS A 517 GLN B 745 ASN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24134 Z= 0.264 Angle : 0.532 9.709 32800 Z= 0.274 Chirality : 0.040 0.323 3824 Planarity : 0.004 0.046 4225 Dihedral : 5.723 59.904 3419 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.16 % Favored : 98.80 % Rotamer: Outliers : 4.10 % Allowed : 12.81 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.65 (0.15), residues: 3091 helix: 2.17 (0.12), residues: 1718 sheet: -0.33 (0.25), residues: 418 loop : -0.16 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 540 HIS 0.027 0.001 HIS A 716 PHE 0.015 0.001 PHE C 571 TYR 0.019 0.001 TYR B 817 ARG 0.007 0.000 ARG A1028 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 357 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.8236 (mtp) cc_final: 0.7974 (mtt) REVERT: A 182 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.7766 (m-80) REVERT: A 799 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8392 (t80) REVERT: B 135 THR cc_start: 0.7192 (p) cc_final: 0.6823 (p) REVERT: B 168 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.6599 (mtp180) REVERT: B 710 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6372 (mt-10) REVERT: C 731 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6065 (mp10) REVERT: C 777 TYR cc_start: 0.8487 (m-80) cc_final: 0.8182 (m-80) outliers start: 103 outliers final: 72 residues processed: 421 average time/residue: 0.3227 time to fit residues: 219.3411 Evaluate side-chains 416 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 339 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 731 GLN Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 932 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1009 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-dev-5409/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-dev-5409/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: 70.4908 > 50: distance: 75 - 79: 27.959 distance: 79 - 80: 23.445 distance: 80 - 81: 24.098 distance: 81 - 82: 15.362 distance: 81 - 87: 13.491 distance: 82 - 102: 32.253 distance: 83 - 84: 28.734 distance: 84 - 85: 18.942 distance: 84 - 86: 7.505 distance: 87 - 88: 12.408 distance: 87 - 93: 9.979 distance: 88 - 89: 41.281 distance: 89 - 90: 14.194 distance: 89 - 94: 40.677 distance: 91 - 92: 5.855 distance: 92 - 93: 18.142 distance: 94 - 95: 28.488 distance: 95 - 96: 20.989 distance: 95 - 98: 23.179 distance: 96 - 97: 26.129 distance: 96 - 102: 17.708 distance: 97 - 118: 12.829 distance: 102 - 103: 5.782 distance: 103 - 104: 3.137 distance: 103 - 106: 32.168 distance: 104 - 105: 11.291 distance: 104 - 110: 11.138 distance: 105 - 126: 41.831 distance: 106 - 107: 4.586 distance: 107 - 108: 29.838 distance: 107 - 109: 7.084 distance: 110 - 111: 3.325 distance: 111 - 112: 24.570 distance: 111 - 114: 20.498 distance: 112 - 113: 28.979 distance: 112 - 118: 14.381 distance: 114 - 115: 51.934 distance: 114 - 116: 44.418 distance: 115 - 117: 9.161 distance: 118 - 119: 30.885 distance: 119 - 120: 18.235 distance: 119 - 122: 26.695 distance: 120 - 121: 24.698 distance: 120 - 126: 19.354 distance: 123 - 124: 34.011 distance: 123 - 125: 11.758 distance: 126 - 127: 29.401 distance: 127 - 128: 14.618 distance: 127 - 130: 17.144 distance: 128 - 129: 4.233 distance: 130 - 131: 22.312 distance: 131 - 132: 17.796 distance: 131 - 133: 28.262 distance: 134 - 135: 8.776 distance: 135 - 136: 13.199 distance: 135 - 138: 21.226 distance: 136 - 137: 23.230 distance: 136 - 148: 20.477 distance: 138 - 139: 25.468 distance: 139 - 140: 3.287 distance: 139 - 141: 16.994 distance: 140 - 142: 23.667 distance: 141 - 143: 39.139 distance: 141 - 144: 28.550 distance: 142 - 143: 37.871 distance: 143 - 145: 39.986 distance: 144 - 146: 12.202 distance: 145 - 147: 11.233 distance: 146 - 147: 22.042 distance: 148 - 149: 26.773 distance: 149 - 150: 34.640 distance: 149 - 152: 25.437 distance: 150 - 160: 52.066 distance: 152 - 153: 11.236 distance: 153 - 154: 11.277 distance: 153 - 155: 32.963 distance: 155 - 157: 3.091 distance: 156 - 158: 39.797 distance: 157 - 158: 14.246 distance: 160 - 161: 26.045 distance: 160 - 187: 26.486 distance: 161 - 162: 29.682 distance: 161 - 164: 22.301 distance: 162 - 163: 10.117 distance: 162 - 167: 22.853 distance: 163 - 184: 26.670 distance: 164 - 165: 3.730