Starting phenix.real_space_refine on Sun Aug 24 12:11:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tnm_26014/08_2025/7tnm_26014.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnm_26014/08_2025/7tnm_26014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tnm_26014/08_2025/7tnm_26014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnm_26014/08_2025/7tnm_26014.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tnm_26014/08_2025/7tnm_26014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnm_26014/08_2025/7tnm_26014.map" } resolution = 4.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 136 5.16 5 Cl 4 4.86 5 C 12570 2.51 5 N 3144 2.21 5 O 3594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19448 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4831 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "B" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4835 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "C" Number of atoms: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4831 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "D" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4835 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.52, per 1000 atoms: 0.18 Number of scatterers: 19448 At special positions: 0 Unit cell: (122.01, 117.03, 135.29, 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) Cl 4 17.00 S 136 16.00 O 3594 8.00 N 3144 7.00 C 12570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.03 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1076 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.03 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.03 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 746.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 24 sheets defined 56.4% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.751A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 488 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 545 Processing helix chain 'A' and resid 565 through 569 removed outlier: 4.130A pdb=" N ASN A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 565 through 569' Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 625 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.685A pdb=" N SER A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 770 Processing helix chain 'A' and resid 792 through 820 removed outlier: 3.639A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1028 Processing helix chain 'A' and resid 1091 through 1103 Processing helix chain 'A' and resid 1104 through 1123 Processing helix chain 'A' and resid 1132 through 1161 Processing helix chain 'A' and resid 1176 through 1209 Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.531A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 482 through 489 removed outlier: 3.715A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 545 Processing helix chain 'B' and resid 564 through 568 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 617 Processing helix chain 'B' and resid 620 through 624 Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 769 Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 789 through 791 No H-bonds generated for 'chain 'B' and resid 789 through 791' Processing helix chain 'B' and resid 792 through 819 removed outlier: 3.588A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1029 Processing helix chain 'B' and resid 1039 through 1043 Processing helix chain 'B' and resid 1091 through 1103 removed outlier: 3.538A pdb=" N SER B1103 " --> pdb=" O ALA B1099 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1123 Processing helix chain 'B' and resid 1132 through 1159 Processing helix chain 'B' and resid 1176 through 1209 Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.751A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 488 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 545 Processing helix chain 'C' and resid 565 through 569 removed outlier: 4.131A pdb=" N ASN C 569 " --> pdb=" O SER C 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 565 through 569' Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 625 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 removed outlier: 3.685A pdb=" N SER C 696 " --> pdb=" O ARG C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 770 Processing helix chain 'C' and resid 792 through 820 removed outlier: 3.639A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1028 Processing helix chain 'C' and resid 1091 through 1103 Processing helix chain 'C' and resid 1104 through 1123 Processing helix chain 'C' and resid 1132 through 1161 Processing helix chain 'C' and resid 1176 through 1209 Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.531A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 489 removed outlier: 3.714A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 545 Processing helix chain 'D' and resid 564 through 568 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 617 Processing helix chain 'D' and resid 620 through 624 Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 697 Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 769 removed outlier: 3.501A pdb=" N TYR D 768 " --> pdb=" O ASN D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 780 Processing helix chain 'D' and resid 789 through 791 No H-bonds generated for 'chain 'D' and resid 789 through 791' Processing helix chain 'D' and resid 792 through 819 removed outlier: 3.588A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 1004 through 1029 Processing helix chain 'D' and resid 1039 through 1043 Processing helix chain 'D' and resid 1091 through 1103 removed outlier: 3.538A pdb=" N SER D1103 " --> pdb=" O ALA D1099 " (cutoff:3.500A) Processing helix chain 'D' and resid 1104 through 1123 Processing helix chain 'D' and resid 1132 through 1159 Processing helix chain 'D' and resid 1176 through 1209 Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 498 removed outlier: 4.833A pdb=" N PHE A 491 " --> pdb=" O THR A 736 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR A 736 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LYS A 493 " --> pdb=" O ILE A 734 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE A 734 " --> pdb=" O LYS A 493 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR A 732 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER A 497 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS A 730 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 702 through 705 removed outlier: 3.613A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1058 through 1060 Processing sheet with id=AA6, first strand: chain 'B' and resid 395 through 399 Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.631A pdb=" N ALA B 452 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 682 through 683 removed outlier: 7.658A pdb=" N VAL B 683 " --> pdb=" O TYR B 647 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR B 649 " --> pdb=" O VAL B 683 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 11.241A pdb=" N LEU B 650 " --> pdb=" O GLU B 705 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 682 through 683 removed outlier: 7.658A pdb=" N VAL B 683 " --> pdb=" O TYR B 647 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR B 649 " --> pdb=" O VAL B 683 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 11.241A pdb=" N LEU B 650 " --> pdb=" O GLU B 705 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1056 through 1060 Processing sheet with id=AB3, first strand: chain 'B' and resid 1064 through 1066 Processing sheet with id=AB4, first strand: chain 'C' and resid 440 through 444 Processing sheet with id=AB5, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'C' and resid 489 through 498 removed outlier: 4.833A pdb=" N PHE C 491 " --> pdb=" O THR C 736 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR C 736 " --> pdb=" O PHE C 491 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LYS C 493 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE C 734 " --> pdb=" O LYS C 493 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR C 732 " --> pdb=" O PHE C 495 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER C 497 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS C 730 " --> pdb=" O SER C 497 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 702 through 705 removed outlier: 3.612A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 1058 through 1060 Processing sheet with id=AB9, first strand: chain 'D' and resid 395 through 399 Processing sheet with id=AC1, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC2, first strand: chain 'D' and resid 452 through 453 removed outlier: 3.630A pdb=" N ALA D 452 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 682 through 683 removed outlier: 7.659A pdb=" N VAL D 683 " --> pdb=" O TYR D 647 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR D 649 " --> pdb=" O VAL D 683 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 11.241A pdb=" N LEU D 650 " --> pdb=" O GLU D 705 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 682 through 683 removed outlier: 7.659A pdb=" N VAL D 683 " --> pdb=" O TYR D 647 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR D 649 " --> pdb=" O VAL D 683 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 11.241A pdb=" N LEU D 650 " --> pdb=" O GLU D 705 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 1056 through 1060 Processing sheet with id=AC6, first strand: chain 'D' and resid 1064 through 1066 1117 hydrogen bonds defined for protein. 3243 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: 3.25 Time building geometry restraints manager: 1.76 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: 5439 1.34 - 1.46: 4181 1.46 - 1.58: 10034 1.58 - 1.70: 8 1.70 - 1.82: 220 Bond restraints: 19882 Sorted by residual: bond pdb=" N THR D1049 " pdb=" CA THR D1049 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 6.99e+00 bond pdb=" N THR B1049 " pdb=" CA THR B1049 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.95e+00 bond pdb=" N LYS D1052 " pdb=" CA LYS D1052 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.15e-02 7.56e+03 5.73e+00 bond pdb=" N LYS B1052 " pdb=" CA LYS B1052 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.15e-02 7.56e+03 5.63e+00 bond pdb=" N SER B1050 " pdb=" CA SER B1050 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.61e+00 ... (remaining 19877 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 26042 2.67 - 5.33: 664 5.33 - 8.00: 136 8.00 - 10.66: 20 10.66 - 13.33: 2 Bond angle restraints: 26864 Sorted by residual: angle pdb=" C ARG A1130 " pdb=" N HIS A1131 " pdb=" CA HIS A1131 " ideal model delta sigma weight residual 121.54 131.98 -10.44 1.91e+00 2.74e-01 2.99e+01 angle pdb=" C ARG C1130 " pdb=" N HIS C1131 " pdb=" CA HIS C1131 " ideal model delta sigma weight residual 121.54 131.96 -10.42 1.91e+00 2.74e-01 2.98e+01 angle pdb=" C LYS A1051 " pdb=" N LYS A1052 " pdb=" CA LYS A1052 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.86e+01 angle pdb=" C LYS C1051 " pdb=" N LYS C1052 " pdb=" CA LYS C1052 " ideal model delta sigma weight residual 121.54 131.70 -10.16 1.91e+00 2.74e-01 2.83e+01 angle pdb=" C GLY D1161 " pdb=" N ASP D1162 " pdb=" CA ASP D1162 " ideal model delta sigma weight residual 123.10 128.13 -5.03 9.60e-01 1.09e+00 2.74e+01 ... (remaining 26859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.69: 11389 24.69 - 49.38: 374 49.38 - 74.07: 20 74.07 - 98.76: 13 98.76 - 123.45: 6 Dihedral angle restraints: 11802 sinusoidal: 4670 harmonic: 7132 Sorted by residual: dihedral pdb=" CA PRO D1083 " pdb=" C PRO D1083 " pdb=" N GLU D1084 " pdb=" CA GLU D1084 " ideal model delta harmonic sigma weight residual 180.00 127.09 52.91 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA PRO B1083 " pdb=" C PRO B1083 " pdb=" N GLU B1084 " pdb=" CA GLU B1084 " ideal model delta harmonic sigma weight residual 180.00 127.11 52.89 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 175.81 -82.81 1 1.00e+01 1.00e-02 8.40e+01 ... (remaining 11799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2619 0.082 - 0.164: 324 0.164 - 0.246: 36 0.246 - 0.328: 13 0.328 - 0.410: 6 Chirality restraints: 2998 Sorted by residual: chirality pdb=" CG LEU C1002 " pdb=" CB LEU C1002 " pdb=" CD1 LEU C1002 " pdb=" CD2 LEU C1002 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CG LEU A1002 " pdb=" CB LEU A1002 " pdb=" CD1 LEU A1002 " pdb=" CD2 LEU A1002 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CG LEU A1114 " pdb=" CB LEU A1114 " pdb=" CD1 LEU A1114 " pdb=" CD2 LEU A1114 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 2995 not shown) Planarity restraints: 3314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 513 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C GLY B 513 " -0.043 2.00e-02 2.50e+03 pdb=" O GLY B 513 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL B 514 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 513 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C GLY D 513 " 0.042 2.00e-02 2.50e+03 pdb=" O GLY D 513 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL D 514 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 421 " 0.032 2.00e-02 2.50e+03 1.70e-02 5.76e+00 pdb=" CG TYR A 421 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 421 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 421 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 421 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 421 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 421 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 421 " 0.023 2.00e-02 2.50e+03 ... (remaining 3311 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2019 2.75 - 3.29: 20355 3.29 - 3.83: 32550 3.83 - 4.36: 37672 4.36 - 4.90: 63551 Nonbonded interactions: 156147 Sorted by model distance: nonbonded pdb=" O PHE D1106 " pdb=" OG SER D1147 " model vdw 2.214 3.040 nonbonded pdb=" O PHE B1106 " pdb=" OG SER B1147 " model vdw 2.214 3.040 nonbonded pdb=" O PHE C1106 " pdb=" OG SER C1147 " model vdw 2.252 3.040 nonbonded pdb=" O PHE A1106 " pdb=" OG SER A1147 " model vdw 2.253 3.040 nonbonded pdb=" O PRO C1107 " pdb=" OG SER C1110 " model vdw 2.295 3.040 ... (remaining 156142 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.050 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 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 : 0.007 0.075 19894 Z= 0.299 Angle : 1.077 13.326 26888 Z= 0.588 Chirality : 0.060 0.410 2998 Planarity : 0.006 0.049 3314 Dihedral : 12.009 123.452 7218 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.49 % Allowed : 2.56 % Favored : 96.95 % Rotamer: Outliers : 0.86 % Allowed : 4.74 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.14), residues: 2460 helix: -0.43 (0.11), residues: 1318 sheet: -0.85 (0.37), residues: 150 loop : -1.65 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1098 TYR 0.032 0.003 TYR A 421 PHE 0.036 0.003 PHE D1126 TRP 0.023 0.003 TRP B 767 HIS 0.015 0.003 HIS C1204 Details of bonding type rmsd covalent geometry : bond 0.00656 (19882) covalent geometry : angle 1.07523 (26864) SS BOND : bond 0.00287 ( 12) SS BOND : angle 2.55891 ( 24) hydrogen bonds : bond 0.22957 ( 1109) hydrogen bonds : angle 6.89563 ( 3243) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 179 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.7244 (tt0) cc_final: 0.6741 (tp30) REVERT: A 463 MET cc_start: 0.3776 (ptm) cc_final: 0.3394 (ttm) REVERT: A 474 ILE cc_start: 0.7567 (tt) cc_final: 0.7140 (mp) REVERT: A 478 PRO cc_start: 0.5035 (Cg_endo) cc_final: 0.4806 (Cg_exo) REVERT: A 486 GLU cc_start: 0.8233 (tp30) cc_final: 0.8007 (pt0) REVERT: A 489 ILE cc_start: 0.8137 (pt) cc_final: 0.7765 (pt) REVERT: A 500 ILE cc_start: 0.5864 (mt) cc_final: 0.5190 (mt) REVERT: A 503 MET cc_start: 0.4273 (ttt) cc_final: 0.3855 (ttt) REVERT: A 514 VAL cc_start: 0.8355 (m) cc_final: 0.7906 (m) REVERT: A 527 MET cc_start: 0.7122 (mtt) cc_final: 0.6192 (mpp) REVERT: A 528 CYS cc_start: 0.8896 (m) cc_final: 0.8529 (m) REVERT: A 573 ILE cc_start: 0.8216 (tt) cc_final: 0.8003 (tt) REVERT: A 587 GLN cc_start: 0.6730 (tp40) cc_final: 0.5513 (pt0) REVERT: A 606 TRP cc_start: 0.7270 (m-10) cc_final: 0.6880 (m100) REVERT: A 609 THR cc_start: 0.9303 (m) cc_final: 0.8954 (p) REVERT: A 627 GLU cc_start: 0.3901 (mt-10) cc_final: 0.2861 (pm20) REVERT: A 705 GLU cc_start: 0.5683 (mm-30) cc_final: 0.5414 (mm-30) REVERT: A 721 MET cc_start: 0.5743 (pp-130) cc_final: 0.5223 (mtp) REVERT: A 742 LEU cc_start: 0.5575 (mm) cc_final: 0.5041 (tp) REVERT: A 811 LEU cc_start: 0.8558 (mm) cc_final: 0.8286 (mm) REVERT: A 815 CYS cc_start: 0.7988 (m) cc_final: 0.7637 (p) REVERT: A 1025 ILE cc_start: 0.7984 (mm) cc_final: 0.7712 (tp) REVERT: A 1030 ASP cc_start: 0.7116 (p0) cc_final: 0.6878 (t70) REVERT: A 1059 HIS cc_start: 0.7750 (p-80) cc_final: 0.6472 (p-80) REVERT: A 1169 LYS cc_start: 0.5537 (mtpt) cc_final: 0.5296 (mtmm) REVERT: A 1174 SER cc_start: 0.6190 (p) cc_final: 0.5847 (t) REVERT: A 1191 MET cc_start: 0.7974 (tpp) cc_final: 0.7393 (tpp) REVERT: A 1194 VAL cc_start: 0.7339 (t) cc_final: 0.6975 (t) REVERT: A 1195 LEU cc_start: 0.8346 (mm) cc_final: 0.7986 (mm) outliers start: 6 outliers final: 0 residues processed: 182 average time/residue: 0.0641 time to fit residues: 14.6377 Evaluate side-chains 104 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.192 Evaluate side-chains 193 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 411 ASN cc_start: 0.7330 (p0) cc_final: 0.6039 (m-40) REVERT: B 414 MET cc_start: 0.8174 (mpt) cc_final: 0.7822 (ptt) REVERT: B 442 LEU cc_start: 0.7839 (mt) cc_final: 0.7246 (mt) REVERT: B 463 MET cc_start: 0.2474 (mtm) cc_final: 0.2046 (mtm) REVERT: B 471 LYS cc_start: 0.6431 (tppp) cc_final: 0.5931 (mttp) REVERT: B 486 GLU cc_start: 0.6890 (tp30) cc_final: 0.6359 (pt0) REVERT: B 511 LYS cc_start: 0.7235 (mmpt) cc_final: 0.6884 (mttm) REVERT: B 519 ASP cc_start: 0.8364 (t70) cc_final: 0.8116 (t0) REVERT: B 527 MET cc_start: 0.8577 (ttp) cc_final: 0.8213 (mmt) REVERT: B 538 VAL cc_start: 0.9070 (t) cc_final: 0.8841 (m) REVERT: B 594 ARG cc_start: 0.7875 (ttp-170) cc_final: 0.7518 (ttp-170) REVERT: B 616 TYR cc_start: 0.8441 (t80) cc_final: 0.8164 (t80) REVERT: B 679 PRO cc_start: 0.5498 (Cg_endo) cc_final: 0.4772 (Cg_exo) REVERT: B 688 GLU cc_start: 0.8133 (tt0) cc_final: 0.7719 (tp30) REVERT: B 704 LEU cc_start: 0.7781 (pt) cc_final: 0.7471 (pt) REVERT: B 708 MET cc_start: 0.8289 (tpp) cc_final: 0.7712 (tpp) REVERT: B 710 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7239 (mp0) REVERT: B 713 GLU cc_start: 0.6542 (mt-10) cc_final: 0.5975 (pt0) REVERT: B 714 GLN cc_start: 0.8055 (mm110) cc_final: 0.7620 (mm-40) REVERT: B 720 THR cc_start: 0.5703 (p) cc_final: 0.4743 (p) REVERT: B 752 LYS cc_start: 0.8310 (ttmt) cc_final: 0.8069 (ptpp) REVERT: B 768 TYR cc_start: 0.6598 (m-80) cc_final: 0.6290 (m-10) REVERT: B 769 ASP cc_start: 0.6883 (m-30) cc_final: 0.6515 (t0) REVERT: B 1040 LYS cc_start: 0.4632 (tppt) cc_final: 0.4002 (tppt) REVERT: B 1069 GLU cc_start: 0.6533 (tp30) cc_final: 0.6292 (tp30) REVERT: B 1087 ASP cc_start: 0.5784 (t70) cc_final: 0.5507 (p0) REVERT: B 1116 MET cc_start: 0.8489 (mmt) cc_final: 0.8260 (mmp) REVERT: B 1127 TYR cc_start: 0.5607 (m-10) cc_final: 0.5177 (m-80) REVERT: B 1191 MET cc_start: 0.8608 (mtt) cc_final: 0.8203 (mmm) REVERT: B 1195 LEU cc_start: 0.8827 (mt) cc_final: 0.8614 (mt) outliers start: 3 outliers final: 1 residues processed: 192 average time/residue: 0.0663 time to fit residues: 16.0455 Evaluate side-chains 111 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 HIS C 619 ASN C1081 HIS C1148 ASN C1204 HIS Total number of N/Q/H flips: 5 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN B 726 ASN B 747 ASN B 791 ASN B1081 HIS B1171 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.077517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.059373 restraints weight = 26844.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.061095 restraints weight = 16235.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.062263 restraints weight = 11799.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.063066 restraints weight = 9465.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.063564 restraints weight = 8113.180| |-----------------------------------------------------------------------------| r_work (final): 0.3240 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.075992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.059146 restraints weight = 25058.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.060795 restraints weight = 16319.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.062012 restraints weight = 12027.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.062791 restraints weight = 9666.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.063343 restraints weight = 8292.638| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19894 Z= 0.232 Angle : 0.724 7.211 26888 Z= 0.392 Chirality : 0.044 0.191 2998 Planarity : 0.005 0.064 3314 Dihedral : 8.935 106.250 2790 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.90 % Favored : 95.85 % Rotamer: Outliers : 0.38 % Allowed : 5.17 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.16), residues: 2460 helix: 1.59 (0.13), residues: 1342 sheet: -1.03 (0.36), residues: 156 loop : -1.30 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1130 TYR 0.020 0.002 TYR B 647 PHE 0.038 0.003 PHE B 658 TRP 0.018 0.002 TRP D 578 HIS 0.008 0.002 HIS D1131 Details of bonding type rmsd covalent geometry : bond 0.00488 (19882) covalent geometry : angle 0.72280 (26864) SS BOND : bond 0.00935 ( 12) SS BOND : angle 1.80968 ( 24) hydrogen bonds : bond 0.05042 ( 1109) hydrogen bonds : angle 4.76075 ( 3243) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: C 405 TYR cc_start: 0.8449 (m-80) cc_final: 0.7997 (m-80) REVERT: C 406 VAL cc_start: 0.8683 (t) cc_final: 0.8269 (t) REVERT: C 407 MET cc_start: 0.8155 (ttm) cc_final: 0.7838 (mmm) REVERT: C 413 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7748 (pm20) REVERT: C 474 ILE cc_start: 0.8752 (tt) cc_final: 0.8287 (mp) REVERT: C 517 PHE cc_start: 0.8129 (p90) cc_final: 0.7502 (p90) REVERT: C 521 LEU cc_start: 0.8438 (mm) cc_final: 0.8134 (mm) REVERT: C 579 PHE cc_start: 0.9029 (t80) cc_final: 0.8688 (t80) REVERT: C 585 MET cc_start: 0.9123 (mmt) cc_final: 0.8870 (mmm) REVERT: C 586 GLN cc_start: 0.7507 (tp40) cc_final: 0.7215 (tp40) REVERT: C 587 GLN cc_start: 0.6644 (tp40) cc_final: 0.5889 (pt0) REVERT: C 606 TRP cc_start: 0.8090 (m-10) cc_final: 0.7334 (m100) REVERT: C 609 THR cc_start: 0.8808 (m) cc_final: 0.8601 (p) REVERT: C 619 ASN cc_start: 0.7606 (t0) cc_final: 0.7014 (t0) REVERT: C 708 MET cc_start: 0.6678 (tpt) cc_final: 0.6029 (tpt) REVERT: C 727 LEU cc_start: 0.8030 (mm) cc_final: 0.7782 (mm) REVERT: C 1023 MET cc_start: 0.8611 (mmm) cc_final: 0.8346 (mmm) REVERT: C 1036 ARG cc_start: 0.5971 (mmm160) cc_final: 0.5419 (mmm-85) REVERT: C 1057 MET cc_start: 0.7617 (mmm) cc_final: 0.7398 (mmm) REVERT: C 1066 CYS cc_start: 0.2290 (OUTLIER) cc_final: 0.1910 (m) REVERT: C 1147 SER cc_start: 0.8985 (t) cc_final: 0.8657 (p) REVERT: C 1190 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8868 (mm-30) REVERT: C 1191 MET cc_start: 0.7873 (tpp) cc_final: 0.7336 (tpp) REVERT: C 1195 LEU cc_start: 0.8234 (mm) cc_final: 0.7374 (mm) REVERT: C 1301 GLU cc_start: 0.5795 (tp30) cc_final: 0.4003 (tp30) outliers start: 3 outliers final: 0 residues processed: 150 average time/residue: 0.0508 time to fit residues: 10.2257 Evaluate side-chains 104 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.121 Evaluate side-chains 132 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 395 VAL cc_start: 0.6492 (t) cc_final: 0.6210 (p) REVERT: B 408 MET cc_start: 0.6185 (mtt) cc_final: 0.4596 (tmm) REVERT: B 414 MET cc_start: 0.7724 (mpp) cc_final: 0.7361 (ptt) REVERT: B 442 LEU cc_start: 0.7761 (mt) cc_final: 0.7555 (pp) REVERT: B 471 LYS cc_start: 0.6677 (tppp) cc_final: 0.6363 (tttt) REVERT: B 496 MET cc_start: 0.7681 (ttp) cc_final: 0.7409 (tpp) REVERT: B 504 ILE cc_start: 0.7737 (pt) cc_final: 0.7159 (pt) REVERT: B 511 LYS cc_start: 0.6992 (mmpt) cc_final: 0.6443 (mttm) REVERT: B 519 ASP cc_start: 0.8490 (t70) cc_final: 0.8280 (t70) REVERT: B 594 ARG cc_start: 0.7804 (ttp-170) cc_final: 0.7404 (ttp-170) REVERT: B 688 GLU cc_start: 0.8130 (tt0) cc_final: 0.7697 (tp30) REVERT: B 704 LEU cc_start: 0.7922 (pt) cc_final: 0.7685 (pt) REVERT: B 708 MET cc_start: 0.7960 (tpp) cc_final: 0.7660 (tpp) REVERT: B 813 GLU cc_start: 0.7054 (tp30) cc_final: 0.6708 (tp30) REVERT: B 1046 GLU cc_start: 0.5411 (mp0) cc_final: 0.5146 (tm-30) REVERT: B 1068 LEU cc_start: 0.7370 (pp) cc_final: 0.6753 (pp) REVERT: B 1069 GLU cc_start: 0.6445 (tp30) cc_final: 0.5963 (mp0) REVERT: B 1082 PHE cc_start: 0.7137 (m-80) cc_final: 0.6742 (m-80) REVERT: B 1116 MET cc_start: 0.8355 (mmt) cc_final: 0.8065 (mmp) REVERT: B 1187 ILE cc_start: 0.8752 (mt) cc_final: 0.8414 (mt) REVERT: B 1191 MET cc_start: 0.8574 (mtt) cc_final: 0.8229 (mmm) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.0545 time to fit residues: 9.6121 Evaluate side-chains 86 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.4431 > 50: distance: 0 - 1: 15.549 distance: 1 - 2: 10.645 distance: 1 - 4: 12.265 distance: 2 - 3: 17.241 distance: 2 - 8: 11.597 distance: 4 - 5: 3.029 distance: 5 - 6: 7.886 distance: 8 - 9: 20.640 distance: 9 - 10: 14.933 distance: 10 - 11: 32.022 distance: 10 - 17: 24.970 distance: 12 - 13: 14.056 distance: 13 - 14: 6.240 distance: 14 - 15: 6.341 distance: 14 - 16: 8.167 distance: 17 - 18: 36.134 distance: 18 - 19: 10.303 distance: 19 - 20: 9.012 distance: 19 - 21: 15.653 distance: 21 - 22: 9.587 distance: 22 - 23: 6.341 distance: 22 - 25: 4.178 distance: 23 - 24: 5.379 distance: 25 - 26: 17.952 distance: 26 - 27: 19.651 distance: 26 - 28: 17.898 distance: 29 - 30: 5.233 distance: 30 - 33: 3.426 distance: 31 - 40: 4.633 distance: 34 - 36: 3.177 distance: 35 - 37: 3.351 distance: 40 - 41: 4.413 distance: 41 - 42: 3.223 distance: 41 - 44: 4.721 distance: 42 - 43: 3.659 distance: 42 - 49: 13.467 distance: 44 - 45: 8.101 distance: 45 - 46: 10.059 distance: 46 - 47: 5.894 distance: 47 - 48: 4.377 distance: 49 - 50: 9.260 distance: 50 - 51: 12.307 distance: 51 - 52: 15.687 distance: 51 - 53: 3.722 distance: 54 - 55: 13.166 distance: 54 - 57: 27.989 distance: 55 - 56: 28.957 distance: 55 - 61: 28.258 distance: 57 - 58: 48.520 distance: 58 - 59: 50.443 distance: 58 - 60: 33.756 distance: 61 - 62: 13.925 distance: 62 - 63: 13.285 distance: 62 - 65: 25.153 distance: 63 - 64: 10.137 distance: 63 - 67: 27.229 distance: 65 - 66: 22.285 distance: 67 - 68: 26.332 distance: 68 - 69: 23.653 distance: 68 - 71: 16.449 distance: 69 - 70: 18.809 distance: 71 - 72: 10.945