Starting phenix.real_space_refine on Tue Jun 25 17:03:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq2_29375/06_2024/8fq2_29375_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq2_29375/06_2024/8fq2_29375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq2_29375/06_2024/8fq2_29375.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq2_29375/06_2024/8fq2_29375.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq2_29375/06_2024/8fq2_29375_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq2_29375/06_2024/8fq2_29375_updated.pdb" } resolution = 3.14 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= 0.003 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 64 5.16 5 Cl 4 4.86 5 C 5338 2.51 5 N 1386 2.21 5 O 1598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A GLU 637": "OE1" <-> "OE2" Residue "A TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C GLU 637": "OE1" <-> "OE2" Residue "C TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1301": "OE1" <-> "OE2" Residue "B GLU 1301": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8390 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2115 Classifications: {'peptide': 270} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Chain: "B" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2115 Classifications: {'peptide': 270} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Chain: "C" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 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: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 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} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 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} Time building chain proxies: 5.32, per 1000 atoms: 0.63 Number of scatterers: 8390 At special positions: 0 Unit cell: (118.755, 90.909, 85.176, 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 64 16.00 O 1598 8.00 N 1386 7.00 C 5338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.6 seconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 16 sheets defined 34.4% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 636 through 641 removed outlier: 3.658A pdb=" N LYS A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 743 through 756 Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'D' and resid 424 through 435 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 637 through 641 removed outlier: 3.867A pdb=" N LYS D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 637 through 641' Processing helix chain 'D' and resid 654 through 660 Processing helix chain 'D' and resid 665 through 675 Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 743 through 756 Processing helix chain 'D' and resid 758 through 767 Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 637 through 641 removed outlier: 3.867A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 637 through 641' Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 743 through 756 Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 636 through 641 removed outlier: 3.658A pdb=" N LYS C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 Processing helix chain 'C' and resid 665 through 675 Processing helix chain 'C' and resid 686 through 696 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 743 through 756 Processing helix chain 'C' and resid 758 through 767 Processing sheet with id= A, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= B, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= C, first strand: chain 'A' and resid 496 through 499 removed outlier: 4.359A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 720 through 723 removed outlier: 4.247A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 395 through 399 removed outlier: 3.656A pdb=" N LYS D 441 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= G, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.730A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS D 730 " --> pdb=" O LEU D 498 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 720 through 723 removed outlier: 4.136A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 395 through 399 removed outlier: 3.657A pdb=" N LYS B 441 " --> pdb=" O VAL B 395 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= K, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.731A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS B 730 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 720 through 723 removed outlier: 4.136A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= N, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= O, first strand: chain 'C' and resid 496 through 499 removed outlier: 4.359A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 720 through 723 removed outlier: 4.246A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) 256 hydrogen bonds defined for protein. 768 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: 1.93 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2630 1.35 - 1.48: 2046 1.48 - 1.60: 3726 1.60 - 1.73: 40 1.73 - 1.85: 104 Bond restraints: 8546 Sorted by residual: bond pdb=" C3 CYZ D1302 " pdb=" C4 CYZ D1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ B1302 " pdb=" C4 CYZ B1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CYZ D1302 " pdb=" C6 CYZ D1302 " ideal model delta sigma weight residual 1.553 1.330 0.223 2.00e-02 2.50e+03 1.24e+02 ... (remaining 8541 not shown) Histogram of bond angle deviations from ideal: 91.81 - 100.25: 24 100.25 - 108.70: 372 108.70 - 117.15: 5772 117.15 - 125.59: 5254 125.59 - 134.04: 106 Bond angle restraints: 11528 Sorted by residual: angle pdb=" CA MET C 407 " pdb=" CB MET C 407 " pdb=" CG MET C 407 " ideal model delta sigma weight residual 114.10 121.59 -7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" CA MET A 407 " pdb=" CB MET A 407 " pdb=" CG MET A 407 " ideal model delta sigma weight residual 114.10 121.56 -7.46 2.00e+00 2.50e-01 1.39e+01 angle pdb=" C9 CYZ A1302 " pdb=" S1 CYZ A1302 " pdb=" N1 CYZ A1302 " ideal model delta sigma weight residual 101.75 111.50 -9.75 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C9 CYZ C1302 " pdb=" S1 CYZ C1302 " pdb=" N1 CYZ C1302 " ideal model delta sigma weight residual 101.75 111.44 -9.69 3.00e+00 1.11e-01 1.04e+01 angle pdb=" CB GLU D 416 " pdb=" CG GLU D 416 " pdb=" CD GLU D 416 " ideal model delta sigma weight residual 112.60 118.04 -5.44 1.70e+00 3.46e-01 1.02e+01 ... (remaining 11523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.96: 4880 22.96 - 45.91: 314 45.91 - 68.87: 32 68.87 - 91.83: 20 91.83 - 114.79: 10 Dihedral angle restraints: 5256 sinusoidal: 2204 harmonic: 3052 Sorted by residual: dihedral pdb=" N2 CYZ C1302 " pdb=" C8 CYZ C1302 " pdb=" N1 CYZ C1302 " pdb=" S1 CYZ C1302 " ideal model delta sinusoidal sigma weight residual 55.73 -59.06 114.79 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" N2 CYZ A1302 " pdb=" C8 CYZ A1302 " pdb=" N1 CYZ A1302 " pdb=" S1 CYZ A1302 " ideal model delta sinusoidal sigma weight residual 55.73 -58.98 114.71 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" N2 CYZ D1302 " pdb=" C8 CYZ D1302 " pdb=" N1 CYZ D1302 " pdb=" S1 CYZ D1302 " ideal model delta sinusoidal sigma weight residual 55.73 -56.68 112.41 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 5253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1167 0.084 - 0.169: 101 0.169 - 0.253: 0 0.253 - 0.338: 0 0.338 - 0.422: 16 Chirality restraints: 1284 Sorted by residual: chirality pdb=" C2 CYZ B1302 " pdb=" C1 CYZ B1302 " pdb=" C3 CYZ B1302 " pdb=" C7 CYZ B1302 " both_signs ideal model delta sigma weight residual False 3.31 2.89 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C8 CYZ C1302 " pdb=" C1 CYZ C1302 " pdb=" N1 CYZ C1302 " pdb=" N2 CYZ C1302 " both_signs ideal model delta sigma weight residual False 2.20 2.63 -0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C2 CYZ C1302 " pdb=" C1 CYZ C1302 " pdb=" C3 CYZ C1302 " pdb=" C7 CYZ C1302 " both_signs ideal model delta sigma weight residual False 3.31 2.89 0.42 2.00e-01 2.50e+01 4.45e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 695 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.92e+00 pdb=" C LYS D 695 " 0.024 2.00e-02 2.50e+03 pdb=" O LYS D 695 " -0.009 2.00e-02 2.50e+03 pdb=" N SER D 696 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 695 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C LYS B 695 " 0.024 2.00e-02 2.50e+03 pdb=" O LYS B 695 " -0.009 2.00e-02 2.50e+03 pdb=" N SER B 696 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 660 " -0.083 9.50e-02 1.11e+02 3.75e-02 1.12e+00 pdb=" NE ARG D 660 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG D 660 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG D 660 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 660 " -0.000 2.00e-02 2.50e+03 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1394 2.77 - 3.30: 7913 3.30 - 3.83: 13863 3.83 - 4.37: 16441 4.37 - 4.90: 28498 Nonbonded interactions: 68109 Sorted by model distance: nonbonded pdb=" OE1 GLU A 705 " pdb=" OH TYR A 732 " model vdw 2.235 2.440 nonbonded pdb=" OE1 GLU C 705 " pdb=" OH TYR C 732 " model vdw 2.235 2.440 nonbonded pdb=" O ARG D 692 " pdb=" OG SER D 696 " model vdw 2.265 2.440 nonbonded pdb=" O ARG B 692 " pdb=" OG SER B 696 " model vdw 2.266 2.440 nonbonded pdb=" OG SER C 497 " pdb=" O2 CYZ C1302 " model vdw 2.273 2.440 ... (remaining 68104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 715 or (resid 716 and (name N or name CA \ or name C or name O or name CB )) or resid 717 through 773 or resid 1301 or resi \ d 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'D' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 715 or (resid 716 and (name N or name CA \ or name C or name O or name CB )) or resid 717 through 773 or resid 1301 or resi \ d 1302)) } 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: 3.370 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: 0.000 Extract box with map and model: 10.100 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.690 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 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 : 0.015 0.243 8546 Z= 0.823 Angle : 0.757 9.755 11528 Z= 0.332 Chirality : 0.062 0.422 1284 Planarity : 0.003 0.037 1422 Dihedral : 15.953 114.786 3296 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.67 % Allowed : 0.45 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.25), residues: 1044 helix: 0.66 (0.26), residues: 380 sheet: -0.24 (0.38), residues: 190 loop : -1.29 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 767 HIS 0.002 0.001 HIS C 412 PHE 0.013 0.001 PHE A 438 TYR 0.014 0.001 TYR A 647 ARG 0.009 0.000 ARG D 660 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 0.854 Fit side-chains REVERT: D 503 MET cc_start: 0.6505 (ttm) cc_final: 0.6265 (ttm) REVERT: B 503 MET cc_start: 0.6510 (ttm) cc_final: 0.6256 (ttm) outliers start: 6 outliers final: 2 residues processed: 143 average time/residue: 0.2276 time to fit residues: 43.5347 Evaluate side-chains 125 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain B residue 644 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.3072 > 50: distance: 9 - 15: 15.982 distance: 15 - 16: 8.213 distance: 16 - 17: 22.368 distance: 16 - 19: 26.080 distance: 17 - 24: 56.460 distance: 19 - 20: 24.928 distance: 20 - 21: 31.890 distance: 21 - 22: 6.592 distance: 21 - 23: 13.894 distance: 24 - 25: 54.471 distance: 25 - 26: 34.107 distance: 25 - 28: 3.517 distance: 26 - 27: 5.948 distance: 26 - 30: 3.621 distance: 28 - 29: 39.576 distance: 30 - 31: 8.465 distance: 30 - 36: 7.579 distance: 31 - 32: 5.168 distance: 31 - 34: 8.260 distance: 32 - 33: 8.391 distance: 34 - 35: 5.105 distance: 35 - 36: 11.597 distance: 37 - 38: 4.124 distance: 38 - 39: 8.812 distance: 38 - 41: 10.386 distance: 39 - 49: 38.192 distance: 41 - 42: 11.187 distance: 42 - 43: 15.308 distance: 42 - 44: 9.626 distance: 43 - 45: 9.510 distance: 44 - 46: 9.308 distance: 45 - 47: 9.717 distance: 46 - 47: 17.167 distance: 47 - 48: 8.574 distance: 49 - 50: 24.201 distance: 50 - 51: 45.513 distance: 50 - 53: 29.174 distance: 51 - 52: 30.404 distance: 51 - 56: 18.572 distance: 53 - 54: 11.902 distance: 53 - 55: 21.180 distance: 56 - 57: 14.223 distance: 57 - 58: 16.265 distance: 57 - 60: 10.046 distance: 58 - 59: 13.413 distance: 58 - 64: 18.858 distance: 60 - 61: 28.403 distance: 61 - 62: 3.053 distance: 64 - 65: 13.285 distance: 65 - 66: 18.535 distance: 65 - 68: 26.937 distance: 66 - 67: 12.961 distance: 66 - 72: 28.350 distance: 68 - 69: 17.905 distance: 69 - 70: 22.802 distance: 70 - 71: 32.545 distance: 72 - 73: 8.177 distance: 73 - 74: 14.085 distance: 73 - 76: 18.599 distance: 74 - 81: 20.989 distance: 77 - 78: 20.083 distance: 78 - 79: 13.874 distance: 79 - 80: 5.048 distance: 81 - 82: 10.494 distance: 82 - 83: 24.322 distance: 82 - 85: 10.368 distance: 83 - 84: 7.397 distance: 83 - 90: 38.205 distance: 85 - 86: 20.817 distance: 86 - 87: 10.764 distance: 87 - 88: 44.788 distance: 88 - 89: 34.215 distance: 90 - 91: 7.187 distance: 91 - 92: 11.899 distance: 92 - 93: 16.005 distance: 92 - 98: 26.179 distance: 95 - 96: 34.943