Starting phenix.real_space_refine on Sat Aug 23 13:48:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7by0_30239/08_2025/7by0_30239.cif Found real_map, /net/cci-nas-00/data/ceres_data/7by0_30239/08_2025/7by0_30239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7by0_30239/08_2025/7by0_30239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7by0_30239/08_2025/7by0_30239.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7by0_30239/08_2025/7by0_30239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7by0_30239/08_2025/7by0_30239.map" } resolution = 4.5 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 12 5.16 5 C 7083 2.51 5 N 2407 2.21 5 O 2903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 12693 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 854 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "B" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 629 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 854 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "F" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 629 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2914 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "J" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2949 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "K" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 363 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TPO:plan-1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "L" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 366 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TPO:plan-1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 2.50, per 1000 atoms: 0.20 Number of scatterers: 12693 At special positions: 0 Unit cell: (86.9, 123.2, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 288 15.00 O 2903 8.00 N 2407 7.00 C 7083 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 - 3.00 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: 0.76 Conformation dependent library (CDL) restraints added in 311.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1628 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 65.6% alpha, 1.2% beta 140 base pairs and 240 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.595A pdb=" N PHE A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N CYS A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 117 removed outlier: 3.582A pdb=" N ALA A 117 " --> pdb=" O CYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.766A pdb=" N LEU A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 4.042A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.828A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.624A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 71 removed outlier: 4.491A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.827A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 47 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.611A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.870A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 80 removed outlier: 3.543A pdb=" N PHE E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE E 75 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 117 removed outlier: 3.558A pdb=" N LEU E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 133 removed outlier: 3.641A pdb=" N LEU E 127 " --> pdb=" O TYR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 138 removed outlier: 4.000A pdb=" N GLN E 137 " --> pdb=" O ARG E 134 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY E 138 " --> pdb=" O GLY E 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 134 through 138' Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.680A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.953A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.514A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.402A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.955A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.606A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.724A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 629 through 640 removed outlier: 3.964A pdb=" N LYS K 633 " --> pdb=" O HIS K 629 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU K 636 " --> pdb=" O ILE K 632 " (cutoff:3.500A) Processing helix chain 'L' and resid 629 through 640 removed outlier: 4.107A pdb=" N LYS L 633 " --> pdb=" O HIS L 629 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 97 removed outlier: 7.069A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.390A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'E' and resid 86 through 87 removed outlier: 7.150A pdb=" N ARG E 86 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.433A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 385 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 720 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 240 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2364 1.33 - 1.45: 4427 1.45 - 1.57: 6115 1.57 - 1.69: 576 1.69 - 1.81: 20 Bond restraints: 13502 Sorted by residual: bond pdb=" OG1 TPO K 651 " pdb=" P TPO K 651 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" OG1 TPO L 651 " pdb=" P TPO L 651 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C1' DA J 165 " pdb=" N9 DA J 165 " ideal model delta sigma weight residual 1.460 1.370 0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" O3P TPO K 651 " pdb=" P TPO K 651 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O3P TPO L 651 " pdb=" P TPO L 651 " ideal model delta sigma weight residual 1.528 1.608 -0.080 2.00e-02 2.50e+03 1.59e+01 ... (remaining 13497 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 18820 2.36 - 4.73: 608 4.73 - 7.09: 33 7.09 - 9.45: 10 9.45 - 11.81: 2 Bond angle restraints: 19473 Sorted by residual: angle pdb=" CB TPO L 651 " pdb=" OG1 TPO L 651 " pdb=" P TPO L 651 " ideal model delta sigma weight residual 119.31 107.50 11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CB TPO K 651 " pdb=" OG1 TPO K 651 " pdb=" P TPO K 651 " ideal model delta sigma weight residual 119.31 107.64 11.67 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C3' DT J 285 " pdb=" C2' DT J 285 " pdb=" C1' DT J 285 " ideal model delta sigma weight residual 101.60 95.99 5.61 1.50e+00 4.44e-01 1.40e+01 angle pdb=" C3' DG I 100 " pdb=" C2' DG I 100 " pdb=" C1' DG I 100 " ideal model delta sigma weight residual 101.60 96.61 4.99 1.50e+00 4.44e-01 1.11e+01 angle pdb=" C3' DA I 68 " pdb=" C2' DA I 68 " pdb=" C1' DA I 68 " ideal model delta sigma weight residual 101.60 96.64 4.96 1.50e+00 4.44e-01 1.09e+01 ... (remaining 19468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 4790 22.35 - 44.69: 1469 44.69 - 67.04: 1002 67.04 - 89.39: 115 89.39 - 111.74: 8 Dihedral angle restraints: 7384 sinusoidal: 4864 harmonic: 2520 Sorted by residual: dihedral pdb=" CA ARG E 41 " pdb=" C ARG E 41 " pdb=" N TYR E 42 " pdb=" CA TYR E 42 " ideal model delta harmonic sigma weight residual -180.00 -154.07 -25.93 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 155.40 24.60 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA LEU K 662 " pdb=" C LEU K 662 " pdb=" N LYS K 663 " pdb=" CA LYS K 663 " ideal model delta harmonic sigma weight residual 180.00 158.86 21.14 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 7381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1676 0.058 - 0.115: 442 0.115 - 0.173: 85 0.173 - 0.231: 9 0.231 - 0.289: 1 Chirality restraints: 2213 Sorted by residual: chirality pdb=" CB ILE B 29 " pdb=" CA ILE B 29 " pdb=" CG1 ILE B 29 " pdb=" CG2 ILE B 29 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA LYS F 31 " pdb=" N LYS F 31 " pdb=" C LYS F 31 " pdb=" CB LYS F 31 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB ILE L 660 " pdb=" CA ILE L 660 " pdb=" CG1 ILE L 660 " pdb=" CG2 ILE L 660 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2210 not shown) Planarity restraints: 1473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 120 " 0.035 2.00e-02 2.50e+03 1.55e-02 7.24e+00 pdb=" N9 DG I 120 " -0.035 2.00e-02 2.50e+03 pdb=" C8 DG I 120 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG I 120 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 120 " -0.011 2.00e-02 2.50e+03 pdb=" C6 DG I 120 " 0.007 2.00e-02 2.50e+03 pdb=" O6 DG I 120 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DG I 120 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 120 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 120 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 120 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 120 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 18 " -0.036 2.00e-02 2.50e+03 1.54e-02 7.14e+00 pdb=" N9 DG I 18 " 0.030 2.00e-02 2.50e+03 pdb=" C8 DG I 18 " 0.012 2.00e-02 2.50e+03 pdb=" N7 DG I 18 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 18 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DG I 18 " -0.015 2.00e-02 2.50e+03 pdb=" O6 DG I 18 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 18 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG I 18 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 18 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DG I 18 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 18 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU K 665 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.06e+00 pdb=" C LEU K 665 " 0.046 2.00e-02 2.50e+03 pdb=" O LEU K 665 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU K 666 " -0.015 2.00e-02 2.50e+03 ... (remaining 1470 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 140 2.54 - 3.13: 9094 3.13 - 3.72: 26032 3.72 - 4.31: 32371 4.31 - 4.90: 45647 Nonbonded interactions: 113284 Sorted by model distance: nonbonded pdb=" OE1 GLU C 92 " pdb=" NH1 ARG K 659 " model vdw 1.950 3.120 nonbonded pdb=" OE2 GLU G 92 " pdb=" NH1 ARG L 659 " model vdw 2.048 3.120 nonbonded pdb=" OE1 GLU D 105 " pdb=" N ILE K 660 " model vdw 2.206 3.120 nonbonded pdb=" OG SER G 40 " pdb=" O SER H 87 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR E 80 " pdb=" O VAL E 83 " model vdw 2.254 3.040 ... (remaining 113279 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 11 through 88 or (resid 89 and (name N or name CA or name \ C or name O or name CB )) or resid 90 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 31 through 107 or (resid 108 and (name N or name CA or nam \ e C or name O or name CB )) or resid 109 through 124)) } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 628 through 644 or (resid 645 and (name N or name CA or na \ me C or name O or name CB )) or resid 646 through 679)) } 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 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: 0.580 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.460 Find NCS groups from input model: 0.130 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 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 : 0.008 0.111 13502 Z= 0.361 Angle : 0.966 11.815 19473 Z= 0.564 Chirality : 0.054 0.289 2213 Planarity : 0.007 0.060 1473 Dihedral : 31.228 111.735 5756 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.15 % Allowed : 11.39 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.59 (0.22), residues: 838 helix: -2.11 (0.16), residues: 532 sheet: None (None), residues: 0 loop : -2.64 (0.30), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 92 TYR 0.014 0.002 TYR F 98 PHE 0.015 0.003 PHE E 79 TRP 0.015 0.003 TRP L 668 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00760 (13502) covalent geometry : angle 0.96642 (19473) hydrogen bonds : bond 0.13530 ( 745) hydrogen bonds : angle 5.31064 ( 1869) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.9464 (m-10) cc_final: 0.9137 (m-10) REVERT: A 66 GLN cc_start: 0.9711 (mm-40) cc_final: 0.9315 (mp10) REVERT: A 74 GLU cc_start: 0.8962 (tt0) cc_final: 0.8328 (mt-10) REVERT: A 85 TYR cc_start: 0.9499 (m-80) cc_final: 0.9244 (m-80) REVERT: A 128 GLN cc_start: 0.9521 (mt0) cc_final: 0.9295 (mm-40) REVERT: A 131 ARG cc_start: 0.9357 (ttt-90) cc_final: 0.9132 (ptm160) REVERT: B 60 VAL cc_start: 0.9565 (m) cc_final: 0.9061 (p) REVERT: B 62 LEU cc_start: 0.9796 (mm) cc_final: 0.9568 (pp) REVERT: B 63 GLU cc_start: 0.9469 (mt-10) cc_final: 0.9028 (pt0) REVERT: B 74 GLU cc_start: 0.9478 (tm-30) cc_final: 0.9216 (tm-30) REVERT: B 84 MET cc_start: 0.9404 (mmm) cc_final: 0.8993 (mmm) REVERT: C 36 LYS cc_start: 0.9453 (mtpt) cc_final: 0.9019 (mmtp) REVERT: C 61 GLU cc_start: 0.9089 (tp30) cc_final: 0.8830 (mm-30) REVERT: C 75 LYS cc_start: 0.9786 (mmtt) cc_final: 0.9492 (mmtm) REVERT: C 87 ILE cc_start: 0.9864 (mm) cc_final: 0.9465 (tp) REVERT: C 95 LYS cc_start: 0.9820 (ttmt) cc_final: 0.9505 (tptp) REVERT: D 80 LEU cc_start: 0.9736 (tp) cc_final: 0.9531 (tt) REVERT: D 99 ARG cc_start: 0.9422 (mtt180) cc_final: 0.8805 (ttm110) REVERT: E 55 TYR cc_start: 0.9609 (m-10) cc_final: 0.9364 (m-10) REVERT: E 85 TYR cc_start: 0.9350 (m-10) cc_final: 0.9122 (m-80) REVERT: E 90 MET cc_start: 0.9315 (tmm) cc_final: 0.9022 (ppp) REVERT: E 95 LEU cc_start: 0.9883 (tp) cc_final: 0.9667 (pp) REVERT: E 100 GLU cc_start: 0.9504 (mt-10) cc_final: 0.9294 (mt-10) REVERT: E 128 GLN cc_start: 0.9605 (tt0) cc_final: 0.8823 (tp-100) REVERT: F 31 LYS cc_start: 0.9743 (pptt) cc_final: 0.9510 (ptmm) REVERT: F 59 LYS cc_start: 0.9669 (ttpp) cc_final: 0.9426 (ptmm) REVERT: F 60 VAL cc_start: 0.9472 (m) cc_final: 0.8985 (p) REVERT: F 62 LEU cc_start: 0.9842 (mm) cc_final: 0.9579 (pp) REVERT: F 63 GLU cc_start: 0.9402 (mt-10) cc_final: 0.9033 (mt-10) REVERT: F 74 GLU cc_start: 0.9548 (tt0) cc_final: 0.9147 (tm-30) REVERT: F 79 LYS cc_start: 0.9670 (mmtm) cc_final: 0.8903 (ttpp) REVERT: G 78 ILE cc_start: 0.9717 (mt) cc_final: 0.9336 (tp) REVERT: G 95 LYS cc_start: 0.9794 (tttm) cc_final: 0.9580 (tptm) REVERT: H 68 ASP cc_start: 0.9233 (t70) cc_final: 0.8948 (t0) REVERT: H 71 GLU cc_start: 0.9234 (pp20) cc_final: 0.9027 (pp20) REVERT: H 72 ARG cc_start: 0.9554 (ttm170) cc_final: 0.9329 (ptp-110) REVERT: H 80 LEU cc_start: 0.9463 (tp) cc_final: 0.9090 (tp) REVERT: H 99 ARG cc_start: 0.9499 (mtt90) cc_final: 0.8717 (ttm110) REVERT: L 665 LEU cc_start: 0.9255 (tt) cc_final: 0.9042 (tp) outliers start: 1 outliers final: 1 residues processed: 213 average time/residue: 0.1323 time to fit residues: 37.5638 Evaluate side-chains 143 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 88 GLN A 96 GLN B 25 ASN B 27 GLN C 38 ASN C 104 GLN D 63 ASN D 95 GLN ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN F 27 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN H 49 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.023085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2322 r_free = 0.2322 target = 0.019214 restraints weight = 171191.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2356 r_free = 0.2356 target = 0.019993 restraints weight = 86447.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2381 r_free = 0.2381 target = 0.020525 restraints weight = 53070.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.020901 restraints weight = 36320.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.021183 restraints weight = 26847.481| |-----------------------------------------------------------------------------| r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13502 Z= 0.229 Angle : 0.697 7.963 19473 Z= 0.416 Chirality : 0.042 0.225 2213 Planarity : 0.005 0.049 1473 Dihedral : 34.922 126.092 4104 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.15 % Allowed : 4.53 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.33 (0.27), residues: 838 helix: -0.07 (0.20), residues: 546 sheet: None (None), residues: 0 loop : -2.41 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 54 TYR 0.028 0.002 TYR F 72 PHE 0.009 0.002 PHE E 68 TRP 0.006 0.001 TRP K 668 HIS 0.005 0.001 HIS E 116 Details of bonding type rmsd covalent geometry : bond 0.00475 (13502) covalent geometry : angle 0.69726 (19473) hydrogen bonds : bond 0.06685 ( 745) hydrogen bonds : angle 3.97594 ( 1869) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.9509 (m-10) cc_final: 0.9054 (m-10) REVERT: A 66 GLN cc_start: 0.9720 (mm-40) cc_final: 0.9331 (mp10) REVERT: A 85 TYR cc_start: 0.9551 (m-80) cc_final: 0.9119 (m-80) REVERT: A 96 GLN cc_start: 0.9180 (tp-100) cc_final: 0.8741 (tp40) REVERT: A 97 GLU cc_start: 0.9458 (mt-10) cc_final: 0.8935 (mt-10) REVERT: A 100 GLU cc_start: 0.9303 (mt-10) cc_final: 0.8937 (mt-10) REVERT: B 54 THR cc_start: 0.9828 (p) cc_final: 0.9587 (p) REVERT: B 59 LYS cc_start: 0.9694 (ptmt) cc_final: 0.9419 (ptmm) REVERT: B 62 LEU cc_start: 0.9789 (mm) cc_final: 0.9553 (pp) REVERT: B 63 GLU cc_start: 0.9411 (mt-10) cc_final: 0.8938 (mt-10) REVERT: B 74 GLU cc_start: 0.9449 (tm-30) cc_final: 0.9222 (tm-30) REVERT: B 84 MET cc_start: 0.9410 (mmm) cc_final: 0.9191 (mmt) REVERT: C 36 LYS cc_start: 0.9491 (mtpt) cc_final: 0.9040 (mmtp) REVERT: C 87 ILE cc_start: 0.9757 (mm) cc_final: 0.9412 (tp) REVERT: C 95 LYS cc_start: 0.9832 (ttmt) cc_final: 0.9601 (tptp) REVERT: D 72 ARG cc_start: 0.9576 (ttm170) cc_final: 0.9333 (ptp-110) REVERT: D 99 ARG cc_start: 0.9353 (mtt180) cc_final: 0.8734 (ttm110) REVERT: E 68 PHE cc_start: 0.9561 (t80) cc_final: 0.9348 (t80) REVERT: E 90 MET cc_start: 0.9187 (tmm) cc_final: 0.8945 (tmm) REVERT: E 95 LEU cc_start: 0.9915 (tp) cc_final: 0.9681 (pp) REVERT: E 96 GLN cc_start: 0.9153 (tp40) cc_final: 0.8824 (tp40) REVERT: E 97 GLU cc_start: 0.9367 (tt0) cc_final: 0.8639 (tt0) REVERT: E 100 GLU cc_start: 0.9424 (mt-10) cc_final: 0.9060 (mt-10) REVERT: E 128 GLN cc_start: 0.9697 (OUTLIER) cc_final: 0.9290 (mm-40) REVERT: F 49 LEU cc_start: 0.9579 (mp) cc_final: 0.9220 (mp) REVERT: F 60 VAL cc_start: 0.9604 (m) cc_final: 0.9199 (p) REVERT: F 62 LEU cc_start: 0.9792 (mm) cc_final: 0.9575 (pp) REVERT: F 63 GLU cc_start: 0.9422 (mt-10) cc_final: 0.9079 (mt-10) REVERT: F 74 GLU cc_start: 0.9588 (tt0) cc_final: 0.9171 (tm-30) REVERT: F 79 LYS cc_start: 0.9645 (mptt) cc_final: 0.9107 (ttpp) REVERT: G 78 ILE cc_start: 0.9716 (mt) cc_final: 0.9289 (tp) REVERT: G 87 ILE cc_start: 0.9848 (mm) cc_final: 0.9514 (tp) REVERT: G 91 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8824 (mm-30) REVERT: G 111 ILE cc_start: 0.9455 (tp) cc_final: 0.9201 (tp) REVERT: H 59 MET cc_start: 0.8827 (tpt) cc_final: 0.8561 (tpp) REVERT: H 80 LEU cc_start: 0.9659 (tp) cc_final: 0.9289 (tp) REVERT: H 99 ARG cc_start: 0.9502 (mtt90) cc_final: 0.8767 (ttm110) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.1316 time to fit residues: 35.5166 Evaluate side-chains 143 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN B 25 ASN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.022299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2293 r_free = 0.2293 target = 0.018567 restraints weight = 180819.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2327 r_free = 0.2327 target = 0.019315 restraints weight = 89743.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2351 r_free = 0.2351 target = 0.019836 restraints weight = 54810.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2367 r_free = 0.2367 target = 0.020196 restraints weight = 37458.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2380 r_free = 0.2380 target = 0.020464 restraints weight = 27737.390| |-----------------------------------------------------------------------------| r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13502 Z= 0.278 Angle : 0.708 10.457 19473 Z= 0.422 Chirality : 0.041 0.174 2213 Planarity : 0.005 0.049 1473 Dihedral : 34.898 130.191 4104 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.43 (0.28), residues: 838 helix: 0.69 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -2.22 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 92 TYR 0.023 0.002 TYR F 51 PHE 0.010 0.002 PHE E 79 TRP 0.007 0.002 TRP E 87 HIS 0.010 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00587 (13502) covalent geometry : angle 0.70787 (19473) hydrogen bonds : bond 0.07707 ( 745) hydrogen bonds : angle 3.98358 ( 1869) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.9528 (t80) cc_final: 0.8942 (t80) REVERT: A 85 TYR cc_start: 0.9543 (m-80) cc_final: 0.9150 (m-80) REVERT: A 96 GLN cc_start: 0.9108 (tp-100) cc_final: 0.8729 (tp40) REVERT: A 97 GLU cc_start: 0.9474 (mt-10) cc_final: 0.8907 (mt-10) REVERT: A 100 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8999 (mt-10) REVERT: A 137 GLN cc_start: 0.9079 (mp10) cc_final: 0.8528 (mp10) REVERT: B 59 LYS cc_start: 0.9740 (ptmt) cc_final: 0.9279 (ptmm) REVERT: B 62 LEU cc_start: 0.9795 (mm) cc_final: 0.9536 (pp) REVERT: B 63 GLU cc_start: 0.9464 (mt-10) cc_final: 0.8809 (mp0) REVERT: B 72 TYR cc_start: 0.9683 (m-80) cc_final: 0.9398 (m-10) REVERT: B 84 MET cc_start: 0.9471 (mmm) cc_final: 0.9049 (mmm) REVERT: C 36 LYS cc_start: 0.9530 (mtpt) cc_final: 0.9057 (mmtp) REVERT: C 87 ILE cc_start: 0.9764 (mm) cc_final: 0.9423 (tp) REVERT: C 95 LYS cc_start: 0.9831 (ttmt) cc_final: 0.9596 (tptp) REVERT: D 72 ARG cc_start: 0.9629 (ttm170) cc_final: 0.9178 (ptm160) REVERT: D 99 ARG cc_start: 0.9364 (mtt180) cc_final: 0.8770 (ttm110) REVERT: E 51 GLU cc_start: 0.9646 (mm-30) cc_final: 0.9363 (mm-30) REVERT: E 68 PHE cc_start: 0.9574 (t80) cc_final: 0.9342 (t80) REVERT: E 90 MET cc_start: 0.9189 (tmm) cc_final: 0.8915 (tmm) REVERT: E 95 LEU cc_start: 0.9924 (tp) cc_final: 0.9695 (pp) REVERT: E 97 GLU cc_start: 0.9466 (tt0) cc_final: 0.8837 (tt0) REVERT: E 128 GLN cc_start: 0.9708 (tt0) cc_final: 0.9250 (tp40) REVERT: F 74 GLU cc_start: 0.9592 (tt0) cc_final: 0.9140 (tm-30) REVERT: F 79 LYS cc_start: 0.9646 (mptt) cc_final: 0.9410 (mtmt) REVERT: G 78 ILE cc_start: 0.9760 (mt) cc_final: 0.9372 (tp) REVERT: G 87 ILE cc_start: 0.9825 (mm) cc_final: 0.9512 (tp) REVERT: G 91 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8791 (mm-30) REVERT: G 95 LYS cc_start: 0.9651 (tttp) cc_final: 0.9380 (tptt) REVERT: H 71 GLU cc_start: 0.9211 (pp20) cc_final: 0.8989 (pp20) REVERT: H 80 LEU cc_start: 0.9670 (tp) cc_final: 0.9358 (tp) REVERT: H 99 ARG cc_start: 0.9574 (mtt90) cc_final: 0.8827 (ttm110) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1429 time to fit residues: 35.2744 Evaluate side-chains 130 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.022848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2312 r_free = 0.2312 target = 0.019077 restraints weight = 178140.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2347 r_free = 0.2347 target = 0.019832 restraints weight = 87881.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2371 r_free = 0.2371 target = 0.020339 restraints weight = 53274.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.020702 restraints weight = 36492.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.020954 restraints weight = 26911.838| |-----------------------------------------------------------------------------| r_work (final): 0.2392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13502 Z= 0.221 Angle : 0.672 10.975 19473 Z= 0.401 Chirality : 0.041 0.170 2213 Planarity : 0.005 0.046 1473 Dihedral : 34.817 131.679 4104 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.15 % Allowed : 4.09 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.04 (0.28), residues: 838 helix: 1.01 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -2.11 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 661 TYR 0.020 0.001 TYR F 51 PHE 0.010 0.002 PHE C 25 TRP 0.006 0.002 TRP E 87 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00469 (13502) covalent geometry : angle 0.67153 (19473) hydrogen bonds : bond 0.06311 ( 745) hydrogen bonds : angle 3.77426 ( 1869) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.9496 (t80) cc_final: 0.8751 (t80) REVERT: A 74 GLU cc_start: 0.9089 (tt0) cc_final: 0.8637 (mt-10) REVERT: A 85 TYR cc_start: 0.9578 (m-80) cc_final: 0.9122 (m-80) REVERT: A 96 GLN cc_start: 0.9074 (tp-100) cc_final: 0.8736 (tp40) REVERT: A 97 GLU cc_start: 0.9492 (mt-10) cc_final: 0.8909 (mt-10) REVERT: A 100 GLU cc_start: 0.9247 (mt-10) cc_final: 0.9010 (mt-10) REVERT: A 109 ASP cc_start: 0.9171 (m-30) cc_final: 0.8845 (m-30) REVERT: B 59 LYS cc_start: 0.9755 (ptmt) cc_final: 0.9505 (ptmm) REVERT: B 63 GLU cc_start: 0.9431 (mt-10) cc_final: 0.8789 (pt0) REVERT: B 72 TYR cc_start: 0.9733 (m-80) cc_final: 0.9396 (m-10) REVERT: B 84 MET cc_start: 0.9440 (mmm) cc_final: 0.9067 (mmm) REVERT: C 36 LYS cc_start: 0.9538 (mtpt) cc_final: 0.9056 (mmtp) REVERT: C 87 ILE cc_start: 0.9775 (mm) cc_final: 0.9424 (tp) REVERT: C 95 LYS cc_start: 0.9821 (ttmt) cc_final: 0.9599 (tptp) REVERT: C 102 ILE cc_start: 0.9352 (tp) cc_final: 0.8994 (tp) REVERT: D 34 LYS cc_start: 0.8346 (mppt) cc_final: 0.8139 (mmtm) REVERT: D 72 ARG cc_start: 0.9582 (ttm170) cc_final: 0.9132 (ptm160) REVERT: D 99 ARG cc_start: 0.9353 (mtt180) cc_final: 0.8739 (ttm110) REVERT: E 51 GLU cc_start: 0.9635 (mm-30) cc_final: 0.9330 (mm-30) REVERT: E 74 GLU cc_start: 0.9455 (mt-10) cc_final: 0.9101 (mt-10) REVERT: E 90 MET cc_start: 0.9198 (tmm) cc_final: 0.8902 (tmm) REVERT: E 95 LEU cc_start: 0.9926 (tp) cc_final: 0.9680 (pp) REVERT: E 97 GLU cc_start: 0.9407 (tt0) cc_final: 0.8777 (tt0) REVERT: E 100 GLU cc_start: 0.9326 (mt-10) cc_final: 0.9087 (mt-10) REVERT: E 128 GLN cc_start: 0.9706 (tt0) cc_final: 0.8907 (tp-100) REVERT: F 52 GLU cc_start: 0.9698 (mp0) cc_final: 0.9483 (mp0) REVERT: F 59 LYS cc_start: 0.9698 (ptmm) cc_final: 0.9462 (ptmm) REVERT: F 62 LEU cc_start: 0.9808 (mm) cc_final: 0.9585 (pp) REVERT: F 74 GLU cc_start: 0.9576 (tt0) cc_final: 0.9113 (tm-30) REVERT: F 79 LYS cc_start: 0.9640 (mptt) cc_final: 0.9093 (ttpp) REVERT: G 39 TYR cc_start: 0.9259 (m-80) cc_final: 0.9027 (m-80) REVERT: G 78 ILE cc_start: 0.9783 (mt) cc_final: 0.9381 (tp) REVERT: G 91 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8801 (mm-30) REVERT: G 95 LYS cc_start: 0.9626 (tttp) cc_final: 0.9322 (tptt) REVERT: H 80 LEU cc_start: 0.9677 (tp) cc_final: 0.9401 (tp) REVERT: H 99 ARG cc_start: 0.9545 (mtt90) cc_final: 0.8792 (ttm110) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.1418 time to fit residues: 35.1252 Evaluate side-chains 135 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 40 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.022512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2300 r_free = 0.2300 target = 0.018793 restraints weight = 179720.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2334 r_free = 0.2334 target = 0.019537 restraints weight = 87493.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2358 r_free = 0.2358 target = 0.020048 restraints weight = 52721.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.020395 restraints weight = 35795.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.020644 restraints weight = 26528.437| |-----------------------------------------------------------------------------| r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13502 Z= 0.250 Angle : 0.686 12.885 19473 Z= 0.406 Chirality : 0.040 0.168 2213 Planarity : 0.005 0.064 1473 Dihedral : 34.792 131.763 4104 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.07 (0.29), residues: 838 helix: 1.04 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -1.95 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 669 TYR 0.041 0.002 TYR F 51 PHE 0.011 0.002 PHE C 25 TRP 0.005 0.002 TRP L 668 HIS 0.010 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00531 (13502) covalent geometry : angle 0.68582 (19473) hydrogen bonds : bond 0.07013 ( 745) hydrogen bonds : angle 3.81956 ( 1869) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.9502 (t80) cc_final: 0.9081 (t80) REVERT: A 74 GLU cc_start: 0.9125 (tt0) cc_final: 0.8679 (mt-10) REVERT: A 85 TYR cc_start: 0.9617 (m-80) cc_final: 0.9149 (m-80) REVERT: A 96 GLN cc_start: 0.9067 (tp-100) cc_final: 0.8670 (tp40) REVERT: A 97 GLU cc_start: 0.9505 (mt-10) cc_final: 0.8867 (mt-10) REVERT: A 100 GLU cc_start: 0.9268 (mt-10) cc_final: 0.9008 (mt-10) REVERT: A 109 ASP cc_start: 0.9139 (m-30) cc_final: 0.8859 (m-30) REVERT: B 59 LYS cc_start: 0.9753 (ptmt) cc_final: 0.9282 (ptmm) REVERT: B 62 LEU cc_start: 0.9807 (mm) cc_final: 0.9557 (pp) REVERT: B 63 GLU cc_start: 0.9436 (mt-10) cc_final: 0.8759 (mp0) REVERT: B 72 TYR cc_start: 0.9736 (m-80) cc_final: 0.9403 (m-10) REVERT: B 84 MET cc_start: 0.9455 (mmm) cc_final: 0.9184 (mmt) REVERT: C 36 LYS cc_start: 0.9535 (mtpt) cc_final: 0.9101 (mmtp) REVERT: C 64 GLU cc_start: 0.9627 (tt0) cc_final: 0.8262 (tp30) REVERT: C 87 ILE cc_start: 0.9790 (mm) cc_final: 0.9455 (tp) REVERT: C 95 LYS cc_start: 0.9826 (ttmt) cc_final: 0.9596 (tptp) REVERT: C 102 ILE cc_start: 0.9374 (tp) cc_final: 0.8955 (tp) REVERT: D 34 LYS cc_start: 0.8255 (mppt) cc_final: 0.8033 (mmtm) REVERT: D 72 ARG cc_start: 0.9571 (ttm170) cc_final: 0.9115 (ptm160) REVERT: D 99 ARG cc_start: 0.9341 (mtt180) cc_final: 0.8726 (ttm110) REVERT: E 51 GLU cc_start: 0.9627 (mm-30) cc_final: 0.9319 (mm-30) REVERT: E 74 GLU cc_start: 0.9416 (mt-10) cc_final: 0.8928 (mt-10) REVERT: E 85 TYR cc_start: 0.9489 (m-10) cc_final: 0.8998 (m-80) REVERT: E 90 MET cc_start: 0.9202 (tmm) cc_final: 0.8949 (tmm) REVERT: E 95 LEU cc_start: 0.9928 (tp) cc_final: 0.9692 (pp) REVERT: E 97 GLU cc_start: 0.9447 (tt0) cc_final: 0.8752 (tt0) REVERT: E 109 ASP cc_start: 0.9117 (m-30) cc_final: 0.8681 (m-30) REVERT: E 128 GLN cc_start: 0.9627 (tt0) cc_final: 0.9304 (tp-100) REVERT: F 74 GLU cc_start: 0.9602 (tt0) cc_final: 0.9138 (tm-30) REVERT: G 39 TYR cc_start: 0.9299 (m-80) cc_final: 0.9088 (m-80) REVERT: G 78 ILE cc_start: 0.9799 (mt) cc_final: 0.9418 (tp) REVERT: G 95 LYS cc_start: 0.9621 (tttp) cc_final: 0.9319 (tptt) REVERT: H 37 TYR cc_start: 0.9572 (m-80) cc_final: 0.9338 (m-10) REVERT: H 59 MET cc_start: 0.8874 (tpt) cc_final: 0.8660 (tpp) REVERT: H 80 LEU cc_start: 0.9686 (tp) cc_final: 0.9436 (tp) REVERT: H 99 ARG cc_start: 0.9570 (mtt90) cc_final: 0.8790 (ttm110) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1464 time to fit residues: 36.1964 Evaluate side-chains 132 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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 702, in refine_xyz self.minimization_no_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 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( 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 44, in __init__ self.weight = mmtbx.refinement.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 362, 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 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.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/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_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: 59.4036 > 50: distance: 63 - 81: 4.078 distance: 67 - 89: 13.475 distance: 72 - 97: 5.677 distance: 82 - 83: 8.424 distance: 83 - 84: 5.581 distance: 83 - 89: 7.161 distance: 85 - 86: 7.355 distance: 86 - 87: 7.363 distance: 86 - 88: 10.429 distance: 89 - 90: 15.035 distance: 90 - 91: 11.849 distance: 90 - 93: 22.267 distance: 91 - 92: 17.736 distance: 91 - 97: 14.531 distance: 93 - 94: 17.930 distance: 94 - 95: 31.380 distance: 94 - 96: 17.423 distance: 97 - 98: 14.826 distance: 98 - 99: 21.600 distance: 98 - 101: 19.260 distance: 99 - 100: 22.516 distance: 99 - 105: 42.393 distance: 101 - 102: 11.762 distance: 102 - 103: 9.732 distance: 102 - 104: 13.322 distance: 105 - 106: 59.404 distance: 105 - 111: 42.676 distance: 106 - 107: 42.802 distance: 106 - 109: 37.377 distance: 107 - 108: 35.302 distance: 107 - 112: 35.119 distance: 109 - 110: 20.825 distance: 110 - 111: 7.827 distance: 112 - 113: 14.033 distance: 113 - 114: 17.325 distance: 114 - 115: 13.026 distance: 114 - 116: 7.040 distance: 116 - 117: 9.839 distance: 117 - 118: 6.631 distance: 117 - 120: 3.626 distance: 118 - 119: 14.603 distance: 118 - 125: 8.212 distance: 119 - 143: 19.182 distance: 120 - 121: 3.877 distance: 121 - 122: 13.758 distance: 122 - 123: 9.404 distance: 122 - 124: 7.084 distance: 125 - 126: 17.808 distance: 126 - 127: 29.552 distance: 126 - 129: 23.317 distance: 127 - 128: 30.255 distance: 127 - 133: 20.201 distance: 128 - 153: 22.484 distance: 129 - 130: 21.686 distance: 130 - 131: 24.022 distance: 130 - 132: 12.474 distance: 133 - 134: 18.022 distance: 134 - 135: 22.154 distance: 134 - 137: 20.093 distance: 135 - 136: 19.668 distance: 135 - 138: 6.048 distance: 136 - 158: 19.517 distance: 138 - 139: 19.077 distance: 139 - 140: 9.907 distance: 139 - 142: 5.029 distance: 140 - 141: 25.322 distance: 140 - 143: 21.340 distance: 143 - 144: 13.838 distance: 144 - 145: 24.594 distance: 144 - 147: 23.804 distance: 145 - 146: 15.844 distance: 145 - 153: 8.608 distance: 146 - 170: 23.450 distance: 147 - 148: 29.604 distance: 148 - 149: 53.900 distance: 148 - 150: 23.040 distance: 149 - 151: 50.048 distance: 150 - 152: 19.504 distance: 151 - 152: 35.878