Starting phenix.real_space_refine on Wed Jul 30 14:26:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7by0_30239/07_2025/7by0_30239.cif Found real_map, /net/cci-nas-00/data/ceres_data/7by0_30239/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7by0_30239/07_2025/7by0_30239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7by0_30239/07_2025/7by0_30239.map" model { file = "/net/cci-nas-00/data/ceres_data/7by0_30239/07_2025/7by0_30239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7by0_30239/07_2025/7by0_30239.cif" } resolution = 4.5 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= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TPO:plan-1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG: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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TPO:plan-1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 7.68, per 1000 atoms: 0.61 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: 3.10 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 6.29 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: 5.26 Time building geometry restraints manager: 3.73 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.130 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.070 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.240 ------------------------------------------------------------------------------- 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 : 11.25 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 (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: -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 TRP 0.015 0.003 TRP L 668 HIS 0.008 0.002 HIS F 75 PHE 0.015 0.003 PHE E 79 TYR 0.014 0.002 TYR F 98 ARG 0.008 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.13530 ( 745) hydrogen bonds : angle 5.31064 ( 1869) covalent geometry : bond 0.00760 (13502) covalent geometry : angle 0.96642 (19473) *********************** 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 : 0.990 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 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: 0.9316 (mp10) REVERT: A 74 GLU cc_start: 0.8962 (tt0) cc_final: 0.8322 (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: 0.9296 (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: 0.9215 (p) REVERT: B 63 GLU cc_start: 0.9469 (mt-10) cc_final: 0.9160 (mt-10) REVERT: B 74 GLU cc_start: 0.9478 (tm-30) cc_final: 0.9217 (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: 0.8831 (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: 0.8804 (ttm110) REVERT: E 55 TYR cc_start: 0.9609 (m-10) cc_final: 0.9363 (m-10) REVERT: E 85 TYR cc_start: 0.9350 (m-10) cc_final: 0.9131 (m-80) REVERT: E 90 MET cc_start: 0.9315 (tmm) cc_final: 0.9049 (tmm) REVERT: E 95 LEU cc_start: 0.9883 (tp) cc_final: 0.9677 (pp) REVERT: E 100 GLU cc_start: 0.9504 (mt-10) cc_final: 0.9298 (mt-10) REVERT: E 128 GLN cc_start: 0.9605 (tt0) cc_final: 0.9153 (mm-40) REVERT: F 31 LYS cc_start: 0.9743 (pptt) cc_final: 0.9509 (ptmm) REVERT: F 60 VAL cc_start: 0.9472 (m) cc_final: 0.8946 (p) REVERT: F 63 GLU cc_start: 0.9402 (mt-10) cc_final: 0.9077 (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: 0.8926 (ttpp) REVERT: G 95 LYS cc_start: 0.9794 (tttm) cc_final: 0.9578 (tptm) REVERT: H 68 ASP cc_start: 0.9233 (t70) cc_final: 0.8912 (t0) REVERT: H 71 GLU cc_start: 0.9234 (pp20) cc_final: 0.9025 (pp20) REVERT: H 72 ARG cc_start: 0.9554 (ttm170) cc_final: 0.9307 (ptm160) REVERT: H 80 LEU cc_start: 0.9463 (tp) cc_final: 0.9089 (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: 0.9040 (tp) outliers start: 1 outliers final: 1 residues processed: 213 average time/residue: 0.3282 time to fit residues: 92.6505 Evaluate side-chains 141 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 GLN A 88 GLN A 96 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 104 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 95 GLN E 96 GLN ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 112 GLN H 49 HIS K 650 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.022292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2288 r_free = 0.2288 target = 0.018538 restraints weight = 178131.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2322 r_free = 0.2322 target = 0.019291 restraints weight = 90253.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2346 r_free = 0.2346 target = 0.019801 restraints weight = 55661.927| |-----------------------------------------------------------------------------| r_work (final): 0.2343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13502 Z= 0.278 Angle : 0.730 8.404 19473 Z= 0.434 Chirality : 0.042 0.224 2213 Planarity : 0.006 0.048 1473 Dihedral : 35.042 128.426 4104 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.15 % Allowed : 4.67 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.27), residues: 838 helix: -0.02 (0.20), residues: 546 sheet: None (None), residues: 0 loop : -2.38 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 668 HIS 0.006 0.002 HIS B 75 PHE 0.013 0.002 PHE E 68 TYR 0.025 0.002 TYR F 72 ARG 0.004 0.001 ARG H 92 Details of bonding type rmsd hydrogen bonds : bond 0.07922 ( 745) hydrogen bonds : angle 4.14265 ( 1869) covalent geometry : bond 0.00584 (13502) covalent geometry : angle 0.72970 (19473) *********************** 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 189 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 1.086 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 55 TYR cc_start: 0.9516 (m-10) cc_final: 0.9051 (m-10) REVERT: A 66 GLN cc_start: 0.9713 (mm110) cc_final: 0.9320 (mp10) REVERT: A 68 PHE cc_start: 0.9512 (t80) cc_final: 0.8975 (t80) REVERT: A 74 GLU cc_start: 0.9157 (tt0) cc_final: 0.8543 (mt-10) REVERT: A 85 TYR cc_start: 0.9548 (m-80) cc_final: 0.9136 (m-80) REVERT: A 96 GLN cc_start: 0.9170 (tp-100) cc_final: 0.8680 (tp40) REVERT: A 97 GLU cc_start: 0.9495 (mt-10) cc_final: 0.8929 (mt-10) REVERT: A 100 GLU cc_start: 0.9352 (mt-10) cc_final: 0.9024 (mt-10) REVERT: B 53 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8618 (tm-30) REVERT: B 59 LYS cc_start: 0.9705 (ptmt) cc_final: 0.9463 (ptmm) REVERT: B 63 GLU cc_start: 0.9441 (mt-10) cc_final: 0.9036 (mt-10) REVERT: B 84 MET cc_start: 0.9439 (mmm) cc_final: 0.9200 (mmt) REVERT: C 36 LYS cc_start: 0.9518 (mtpt) cc_final: 0.9092 (mmtp) REVERT: C 87 ILE cc_start: 0.9767 (mm) cc_final: 0.9417 (tp) REVERT: C 95 LYS cc_start: 0.9825 (ttmt) cc_final: 0.9625 (tptp) REVERT: D 72 ARG cc_start: 0.9610 (ttm170) cc_final: 0.9369 (ptm160) REVERT: D 95 GLN cc_start: 0.9743 (tt0) cc_final: 0.8758 (tm-30) REVERT: D 99 ARG cc_start: 0.9392 (mtt180) cc_final: 0.8777 (tpp80) REVERT: D 113 GLU cc_start: 0.9646 (mm-30) cc_final: 0.9356 (mt-10) REVERT: E 90 MET cc_start: 0.9233 (tmm) cc_final: 0.8986 (tmm) REVERT: E 95 LEU cc_start: 0.9916 (tp) cc_final: 0.9680 (pp) REVERT: E 96 GLN cc_start: 0.9153 (tp-100) cc_final: 0.8910 (tp40) REVERT: E 97 GLU cc_start: 0.9420 (tt0) cc_final: 0.8775 (tt0) REVERT: E 100 GLU cc_start: 0.9445 (mt-10) cc_final: 0.9163 (mt-10) REVERT: E 128 GLN cc_start: 0.9688 (OUTLIER) cc_final: 0.9292 (mm110) REVERT: E 139 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8833 (mp0) REVERT: F 49 LEU cc_start: 0.9624 (mp) cc_final: 0.9247 (mp) REVERT: F 60 VAL cc_start: 0.9597 (m) cc_final: 0.9180 (p) REVERT: F 63 GLU cc_start: 0.9427 (mt-10) cc_final: 0.9203 (mp0) REVERT: F 74 GLU cc_start: 0.9608 (tt0) cc_final: 0.9185 (tm-30) REVERT: F 79 LYS cc_start: 0.9658 (mptt) cc_final: 0.9114 (ttpp) REVERT: G 73 ASN cc_start: 0.9364 (t0) cc_final: 0.9015 (m110) REVERT: G 87 ILE cc_start: 0.9856 (mm) cc_final: 0.9511 (tp) REVERT: G 91 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8852 (mm-30) REVERT: G 111 ILE cc_start: 0.9465 (tp) cc_final: 0.9214 (tp) REVERT: H 59 MET cc_start: 0.8900 (tpt) cc_final: 0.8585 (tpp) REVERT: H 72 ARG cc_start: 0.9670 (ttm170) cc_final: 0.9370 (ptm160) REVERT: H 80 LEU cc_start: 0.9682 (tp) cc_final: 0.9359 (tp) REVERT: H 99 ARG cc_start: 0.9543 (mtt90) cc_final: 0.8811 (ttm110) REVERT: H 113 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8492 (tm-30) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.4396 time to fit residues: 118.0179 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 : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.022003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2278 r_free = 0.2278 target = 0.018302 restraints weight = 179837.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2312 r_free = 0.2312 target = 0.019044 restraints weight = 88728.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2335 r_free = 0.2335 target = 0.019552 restraints weight = 53920.225| |-----------------------------------------------------------------------------| r_work (final): 0.2329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13502 Z= 0.283 Angle : 0.715 8.839 19473 Z= 0.427 Chirality : 0.041 0.176 2213 Planarity : 0.006 0.052 1473 Dihedral : 35.016 131.970 4104 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % 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 (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: -0.44 (0.28), residues: 838 helix: 0.69 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -2.22 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 87 HIS 0.011 0.002 HIS B 75 PHE 0.008 0.002 PHE G 25 TYR 0.017 0.002 TYR C 57 ARG 0.008 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.07892 ( 745) hydrogen bonds : angle 4.02885 ( 1869) covalent geometry : bond 0.00599 (13502) covalent geometry : angle 0.71465 (19473) *********************** 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 180 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.054 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 66 GLN cc_start: 0.9690 (mm110) cc_final: 0.9318 (mp10) REVERT: A 68 PHE cc_start: 0.9535 (t80) cc_final: 0.9188 (t80) REVERT: A 74 GLU cc_start: 0.9136 (tt0) cc_final: 0.8558 (mt-10) REVERT: A 85 TYR cc_start: 0.9543 (m-80) cc_final: 0.9129 (m-80) REVERT: A 96 GLN cc_start: 0.9091 (tp-100) cc_final: 0.8676 (tp40) REVERT: A 97 GLU cc_start: 0.9494 (mt-10) cc_final: 0.8904 (mt-10) REVERT: A 100 GLU cc_start: 0.9311 (mt-10) cc_final: 0.9043 (mt-10) REVERT: B 53 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8637 (tm-30) REVERT: B 59 LYS cc_start: 0.9728 (ptmt) cc_final: 0.9365 (ptmm) REVERT: B 63 GLU cc_start: 0.9461 (mt-10) cc_final: 0.8975 (mp0) REVERT: B 84 MET cc_start: 0.9479 (mmm) cc_final: 0.9071 (mmm) REVERT: C 36 LYS cc_start: 0.9536 (mtpt) cc_final: 0.9066 (mmtp) REVERT: C 87 ILE cc_start: 0.9786 (mm) cc_final: 0.9433 (tp) REVERT: C 95 LYS cc_start: 0.9834 (ttmt) cc_final: 0.9557 (tptp) REVERT: D 72 ARG cc_start: 0.9657 (ttm170) cc_final: 0.9431 (ptm160) REVERT: D 95 GLN cc_start: 0.9733 (tt0) cc_final: 0.9036 (tt0) REVERT: D 99 ARG cc_start: 0.9383 (mtt180) cc_final: 0.8770 (ttm110) REVERT: E 51 GLU cc_start: 0.9669 (mm-30) cc_final: 0.9369 (mm-30) REVERT: E 68 PHE cc_start: 0.9604 (t80) cc_final: 0.9146 (t80) REVERT: E 74 GLU cc_start: 0.9472 (mt-10) cc_final: 0.9146 (mt-10) REVERT: E 90 MET cc_start: 0.9239 (tmm) cc_final: 0.8954 (tmm) REVERT: E 96 GLN cc_start: 0.9064 (tp-100) cc_final: 0.8770 (tp40) REVERT: E 97 GLU cc_start: 0.9493 (tt0) cc_final: 0.8850 (tt0) REVERT: E 128 GLN cc_start: 0.9718 (tt0) cc_final: 0.9293 (tp40) REVERT: E 139 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8815 (mp0) REVERT: F 59 LYS cc_start: 0.9684 (ptmm) cc_final: 0.9466 (ptmm) REVERT: F 60 VAL cc_start: 0.9580 (m) cc_final: 0.9115 (p) REVERT: F 63 GLU cc_start: 0.9368 (mt-10) cc_final: 0.8899 (mt-10) REVERT: F 74 GLU cc_start: 0.9578 (tt0) cc_final: 0.9138 (tm-30) REVERT: F 79 LYS cc_start: 0.9676 (mptt) cc_final: 0.9175 (ttpp) REVERT: G 73 ASN cc_start: 0.9407 (t0) cc_final: 0.9088 (m110) REVERT: G 91 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8840 (mm-30) REVERT: G 95 LYS cc_start: 0.9683 (tttp) cc_final: 0.9364 (tptm) REVERT: H 59 MET cc_start: 0.8927 (tpt) cc_final: 0.8684 (tpp) REVERT: H 80 LEU cc_start: 0.9700 (tp) cc_final: 0.9413 (tp) REVERT: H 99 ARG cc_start: 0.9565 (mtt90) cc_final: 0.8802 (ttm110) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.3807 time to fit residues: 92.5890 Evaluate side-chains 134 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.022521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2297 r_free = 0.2297 target = 0.018759 restraints weight = 174029.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2332 r_free = 0.2332 target = 0.019507 restraints weight = 85989.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2356 r_free = 0.2356 target = 0.020022 restraints weight = 52323.053| |-----------------------------------------------------------------------------| r_work (final): 0.2349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13502 Z= 0.245 Angle : 0.685 12.696 19473 Z= 0.407 Chirality : 0.041 0.172 2213 Planarity : 0.005 0.044 1473 Dihedral : 34.937 131.963 4104 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.15 % Allowed : 4.67 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.28), residues: 838 helix: 0.91 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -2.08 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 87 HIS 0.010 0.001 HIS B 75 PHE 0.011 0.002 PHE E 102 TYR 0.018 0.001 TYR F 51 ARG 0.004 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.06941 ( 745) hydrogen bonds : angle 3.81580 ( 1869) covalent geometry : bond 0.00518 (13502) covalent geometry : angle 0.68483 (19473) *********************** 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 : 0.975 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: symmetry clash REVERT: A 68 PHE cc_start: 0.9508 (t80) cc_final: 0.8787 (t80) REVERT: A 85 TYR cc_start: 0.9610 (m-80) cc_final: 0.9147 (m-80) REVERT: A 96 GLN cc_start: 0.9032 (tp-100) cc_final: 0.8778 (tp40) REVERT: A 97 GLU cc_start: 0.9504 (mt-10) cc_final: 0.8993 (mt-10) REVERT: B 53 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8555 (tm-30) REVERT: B 59 LYS cc_start: 0.9756 (ptmt) cc_final: 0.9451 (ptmm) REVERT: B 60 VAL cc_start: 0.9586 (m) cc_final: 0.9050 (p) REVERT: B 63 GLU cc_start: 0.9450 (mt-10) cc_final: 0.8925 (mp0) REVERT: B 72 TYR cc_start: 0.9720 (m-80) cc_final: 0.9387 (m-10) REVERT: B 84 MET cc_start: 0.9446 (mmm) cc_final: 0.9092 (mmm) REVERT: C 36 LYS cc_start: 0.9518 (mtpt) cc_final: 0.9047 (mmtp) REVERT: C 87 ILE cc_start: 0.9789 (mm) cc_final: 0.9427 (tp) REVERT: C 95 LYS cc_start: 0.9826 (ttmt) cc_final: 0.9599 (tptp) REVERT: C 102 ILE cc_start: 0.9340 (tp) cc_final: 0.9128 (tp) REVERT: D 72 ARG cc_start: 0.9654 (ttm170) cc_final: 0.9431 (ptm160) REVERT: D 95 GLN cc_start: 0.9651 (tt0) cc_final: 0.9096 (tt0) REVERT: D 99 ARG cc_start: 0.9361 (mtt180) cc_final: 0.8718 (ttm110) REVERT: E 51 GLU cc_start: 0.9650 (mm-30) cc_final: 0.9355 (mm-30) REVERT: E 74 GLU cc_start: 0.9434 (mt-10) cc_final: 0.9068 (mt-10) REVERT: E 85 TYR cc_start: 0.9531 (m-10) cc_final: 0.9074 (m-80) REVERT: E 90 MET cc_start: 0.9294 (tmm) cc_final: 0.9018 (tmm) REVERT: E 95 LEU cc_start: 0.9903 (tt) cc_final: 0.9681 (pp) REVERT: E 96 GLN cc_start: 0.9299 (tp-100) cc_final: 0.8868 (tm-30) REVERT: E 97 GLU cc_start: 0.9233 (tt0) cc_final: 0.8757 (tt0) REVERT: E 128 GLN cc_start: 0.9715 (tt0) cc_final: 0.9188 (tp-100) REVERT: E 139 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8697 (mp0) REVERT: F 74 GLU cc_start: 0.9567 (tt0) cc_final: 0.9100 (tm-30) REVERT: G 73 ASN cc_start: 0.9422 (t0) cc_final: 0.9124 (m110) REVERT: G 95 LYS cc_start: 0.9671 (tttp) cc_final: 0.9351 (tptm) REVERT: H 80 LEU cc_start: 0.9692 (tp) cc_final: 0.9427 (tp) REVERT: H 99 ARG cc_start: 0.9562 (mtt90) cc_final: 0.8764 (ttm110) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.3197 time to fit residues: 79.4597 Evaluate side-chains 139 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 101 optimal weight: 30.0000 chunk 22 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 40.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 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 = 0.2480 r_free = 0.2480 target = 0.022472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2299 r_free = 0.2299 target = 0.018770 restraints weight = 174177.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2333 r_free = 0.2333 target = 0.019518 restraints weight = 84809.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2357 r_free = 0.2357 target = 0.020025 restraints weight = 50931.842| |-----------------------------------------------------------------------------| r_work (final): 0.2351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.3452 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= 0.231 Angle : 0.669 10.625 19473 Z= 0.398 Chirality : 0.040 0.164 2213 Planarity : 0.005 0.044 1473 Dihedral : 34.861 131.776 4104 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.29), residues: 838 helix: 1.08 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.88 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 87 HIS 0.009 0.001 HIS B 75 PHE 0.011 0.002 PHE C 25 TYR 0.018 0.001 TYR C 57 ARG 0.005 0.000 ARG L 656 Details of bonding type rmsd hydrogen bonds : bond 0.06595 ( 745) hydrogen bonds : angle 3.72323 ( 1869) covalent geometry : bond 0.00491 (13502) covalent geometry : angle 0.66899 (19473) *********************** 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 187 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.044 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.9154 (tt0) cc_final: 0.8646 (mt-10) REVERT: A 85 TYR cc_start: 0.9614 (m-80) cc_final: 0.9143 (m-80) REVERT: A 96 GLN cc_start: 0.9227 (tp-100) cc_final: 0.8895 (tp40) REVERT: A 97 GLU cc_start: 0.9461 (mt-10) cc_final: 0.9177 (mt-10) REVERT: A 109 ASP cc_start: 0.9202 (m-30) cc_final: 0.8915 (m-30) REVERT: B 59 LYS cc_start: 0.9755 (ptmt) cc_final: 0.9408 (ptmm) REVERT: B 63 GLU cc_start: 0.9464 (mt-10) cc_final: 0.8955 (mp0) REVERT: B 72 TYR cc_start: 0.9713 (m-80) cc_final: 0.9382 (m-10) REVERT: C 36 LYS cc_start: 0.9536 (mtpt) cc_final: 0.9055 (mmtp) REVERT: C 102 ILE cc_start: 0.9331 (tp) cc_final: 0.8927 (tp) REVERT: D 34 LYS cc_start: 0.8206 (mppt) cc_final: 0.7962 (mmtm) REVERT: D 72 ARG cc_start: 0.9649 (ttm170) cc_final: 0.9423 (ptm160) REVERT: D 99 ARG cc_start: 0.9348 (mtt180) cc_final: 0.8718 (ttm110) REVERT: E 51 GLU cc_start: 0.9652 (mm-30) cc_final: 0.9380 (mm-30) REVERT: E 74 GLU cc_start: 0.9468 (mt-10) cc_final: 0.9085 (mt-10) REVERT: E 85 TYR cc_start: 0.9518 (m-10) cc_final: 0.8998 (m-80) REVERT: E 90 MET cc_start: 0.9246 (tmm) cc_final: 0.8997 (tmm) REVERT: E 95 LEU cc_start: 0.9891 (tt) cc_final: 0.9689 (pp) REVERT: E 96 GLN cc_start: 0.9353 (tp-100) cc_final: 0.9108 (tp40) REVERT: E 109 ASP cc_start: 0.9117 (m-30) cc_final: 0.8727 (m-30) REVERT: E 128 GLN cc_start: 0.9732 (tt0) cc_final: 0.9200 (tp-100) REVERT: E 139 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8593 (mp0) REVERT: F 74 GLU cc_start: 0.9568 (tt0) cc_final: 0.9116 (tm-30) REVERT: G 73 ASN cc_start: 0.9391 (t0) cc_final: 0.9096 (m110) REVERT: G 95 LYS cc_start: 0.9648 (tttp) cc_final: 0.9337 (tptt) REVERT: H 80 LEU cc_start: 0.9694 (tp) cc_final: 0.9450 (tp) REVERT: H 99 ARG cc_start: 0.9599 (mtt90) cc_final: 0.8753 (ttm110) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2886 time to fit residues: 73.2765 Evaluate side-chains 140 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 83 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 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 HIS ** 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 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.022673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2308 r_free = 0.2308 target = 0.018939 restraints weight = 175098.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2343 r_free = 0.2343 target = 0.019700 restraints weight = 83576.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2367 r_free = 0.2367 target = 0.020216 restraints weight = 49742.794| |-----------------------------------------------------------------------------| r_work (final): 0.2360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13502 Z= 0.220 Angle : 0.669 15.269 19473 Z= 0.392 Chirality : 0.040 0.159 2213 Planarity : 0.005 0.045 1473 Dihedral : 34.836 131.891 4104 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.29), residues: 838 helix: 1.16 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.80 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 87 HIS 0.009 0.001 HIS B 75 PHE 0.010 0.002 PHE C 25 TYR 0.027 0.002 TYR F 51 ARG 0.009 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.06264 ( 745) hydrogen bonds : angle 3.64736 ( 1869) covalent geometry : bond 0.00470 (13502) covalent geometry : angle 0.66923 (19473) *********************** REFINEMENT MACRO_CYCLE 6 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 186 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.932 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.9464 (t80) cc_final: 0.9108 (t80) REVERT: A 74 GLU cc_start: 0.9327 (tt0) cc_final: 0.8627 (mt-10) REVERT: A 85 TYR cc_start: 0.9597 (m-80) cc_final: 0.9115 (m-80) REVERT: A 96 GLN cc_start: 0.9234 (tp-100) cc_final: 0.8876 (tp40) REVERT: A 97 GLU cc_start: 0.9415 (mt-10) cc_final: 0.9210 (mt-10) REVERT: A 109 ASP cc_start: 0.9235 (m-30) cc_final: 0.8948 (m-30) REVERT: A 137 GLN cc_start: 0.9166 (mp10) cc_final: 0.8938 (mp10) REVERT: B 59 LYS cc_start: 0.9751 (ptmt) cc_final: 0.9412 (ptmm) REVERT: B 63 GLU cc_start: 0.9475 (mt-10) cc_final: 0.8952 (mp0) REVERT: B 72 TYR cc_start: 0.9715 (m-80) cc_final: 0.9400 (m-80) REVERT: C 36 LYS cc_start: 0.9535 (mtpt) cc_final: 0.9008 (mmtp) REVERT: C 95 LYS cc_start: 0.9697 (tttp) cc_final: 0.9486 (tptm) REVERT: C 102 ILE cc_start: 0.9365 (tp) cc_final: 0.8916 (tp) REVERT: D 34 LYS cc_start: 0.8258 (mppt) cc_final: 0.8032 (mmtm) REVERT: D 72 ARG cc_start: 0.9642 (ttm170) cc_final: 0.9398 (ptm160) REVERT: D 95 GLN cc_start: 0.9692 (tt0) cc_final: 0.8968 (tt0) REVERT: D 99 ARG cc_start: 0.9321 (mtt180) cc_final: 0.8677 (ttm110) REVERT: E 51 GLU cc_start: 0.9650 (mm-30) cc_final: 0.9381 (mm-30) REVERT: E 68 PHE cc_start: 0.9528 (t80) cc_final: 0.9289 (t80) REVERT: E 85 TYR cc_start: 0.9560 (m-10) cc_final: 0.9025 (m-80) REVERT: E 90 MET cc_start: 0.9208 (tmm) cc_final: 0.8973 (tmm) REVERT: E 95 LEU cc_start: 0.9892 (tt) cc_final: 0.9671 (pp) REVERT: E 97 GLU cc_start: 0.9573 (tt0) cc_final: 0.9049 (tt0) REVERT: E 128 GLN cc_start: 0.9735 (tt0) cc_final: 0.9208 (tp-100) REVERT: E 139 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8572 (mp0) REVERT: F 68 ASP cc_start: 0.9672 (m-30) cc_final: 0.9258 (m-30) REVERT: F 74 GLU cc_start: 0.9593 (tt0) cc_final: 0.9135 (tm-30) REVERT: G 73 ASN cc_start: 0.9402 (t0) cc_final: 0.9082 (m110) REVERT: G 95 LYS cc_start: 0.9640 (tttp) cc_final: 0.9336 (tptt) REVERT: H 59 MET cc_start: 0.8922 (tpt) cc_final: 0.8703 (tpp) REVERT: H 80 LEU cc_start: 0.9667 (tp) cc_final: 0.9414 (tp) REVERT: H 99 ARG cc_start: 0.9549 (mtt90) cc_final: 0.8769 (ttm110) REVERT: H 113 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8712 (tm-30) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2907 time to fit residues: 73.5851 Evaluate side-chains 138 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 chunk 97 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 overall best weight: 4.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 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 64 ASN ** 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 = 0.2489 r_free = 0.2489 target = 0.022682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2307 r_free = 0.2307 target = 0.018944 restraints weight = 177869.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2342 r_free = 0.2342 target = 0.019696 restraints weight = 86392.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2366 r_free = 0.2366 target = 0.020203 restraints weight = 51924.861| |-----------------------------------------------------------------------------| r_work (final): 0.2358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13502 Z= 0.224 Angle : 0.670 12.190 19473 Z= 0.394 Chirality : 0.040 0.155 2213 Planarity : 0.005 0.044 1473 Dihedral : 34.788 131.740 4104 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.29), residues: 838 helix: 1.11 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.69 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP K 668 HIS 0.009 0.001 HIS B 75 PHE 0.012 0.002 PHE E 68 TYR 0.023 0.002 TYR C 57 ARG 0.012 0.001 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.06303 ( 745) hydrogen bonds : angle 3.68093 ( 1869) covalent geometry : bond 0.00478 (13502) covalent geometry : angle 0.67040 (19473) *********************** REFINEMENT MACRO_CYCLE 7 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 184 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.008 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: 0.9444 (t80) cc_final: 0.9048 (t80) REVERT: A 74 GLU cc_start: 0.9296 (tt0) cc_final: 0.8636 (mt-10) REVERT: A 85 TYR cc_start: 0.9602 (m-80) cc_final: 0.9111 (m-80) REVERT: A 96 GLN cc_start: 0.9228 (tp-100) cc_final: 0.8903 (tp40) REVERT: A 97 GLU cc_start: 0.9457 (mt-10) cc_final: 0.9224 (mt-10) REVERT: B 59 LYS cc_start: 0.9747 (ptmt) cc_final: 0.9394 (ptmm) REVERT: B 63 GLU cc_start: 0.9461 (mt-10) cc_final: 0.8949 (mp0) REVERT: B 72 TYR cc_start: 0.9703 (m-80) cc_final: 0.9424 (m-80) REVERT: C 36 LYS cc_start: 0.9536 (mtpt) cc_final: 0.9032 (mmtp) REVERT: C 64 GLU cc_start: 0.9611 (tt0) cc_final: 0.8968 (tt0) REVERT: C 95 LYS cc_start: 0.9690 (tttp) cc_final: 0.9461 (tptm) REVERT: C 102 ILE cc_start: 0.9386 (tp) cc_final: 0.8919 (tp) REVERT: D 57 LYS cc_start: 0.9467 (mmmt) cc_final: 0.9162 (mmmt) REVERT: D 72 ARG cc_start: 0.9626 (ttm170) cc_final: 0.9394 (ptm160) REVERT: D 95 GLN cc_start: 0.9693 (tt0) cc_final: 0.8945 (tt0) REVERT: D 99 ARG cc_start: 0.9328 (mtt180) cc_final: 0.8717 (ttm110) REVERT: E 51 GLU cc_start: 0.9638 (mm-30) cc_final: 0.9362 (mm-30) REVERT: E 60 GLU cc_start: 0.9523 (pm20) cc_final: 0.9319 (pm20) REVERT: E 85 TYR cc_start: 0.9539 (m-10) cc_final: 0.9029 (m-80) REVERT: E 97 GLU cc_start: 0.9550 (tt0) cc_final: 0.9039 (tt0) REVERT: E 128 GLN cc_start: 0.9733 (tt0) cc_final: 0.9096 (tp-100) REVERT: E 139 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8543 (mp0) REVERT: F 68 ASP cc_start: 0.9622 (m-30) cc_final: 0.9420 (m-30) REVERT: F 74 GLU cc_start: 0.9595 (tt0) cc_final: 0.9131 (tm-30) REVERT: G 73 ASN cc_start: 0.9398 (t0) cc_final: 0.9076 (m110) REVERT: G 95 LYS cc_start: 0.9644 (tttp) cc_final: 0.9342 (tptt) REVERT: H 80 LEU cc_start: 0.9676 (tp) cc_final: 0.9423 (tp) REVERT: H 99 ARG cc_start: 0.9547 (mtt90) cc_final: 0.8715 (ttm110) REVERT: K 647 LEU cc_start: 0.9426 (tp) cc_final: 0.9190 (tp) REVERT: K 661 ARG cc_start: 0.9227 (mpp-170) cc_final: 0.8782 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2997 time to fit residues: 74.6931 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 : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 101 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 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 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.022673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2306 r_free = 0.2306 target = 0.018939 restraints weight = 175644.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2342 r_free = 0.2342 target = 0.019692 restraints weight = 84880.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2366 r_free = 0.2366 target = 0.020203 restraints weight = 50962.665| |-----------------------------------------------------------------------------| r_work (final): 0.2359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13502 Z= 0.236 Angle : 0.677 13.640 19473 Z= 0.397 Chirality : 0.040 0.172 2213 Planarity : 0.005 0.048 1473 Dihedral : 34.760 132.079 4104 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.29), residues: 838 helix: 1.11 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.55 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 87 HIS 0.009 0.001 HIS B 75 PHE 0.016 0.002 PHE A 102 TYR 0.024 0.002 TYR C 57 ARG 0.010 0.001 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.06512 ( 745) hydrogen bonds : angle 3.71796 ( 1869) covalent geometry : bond 0.00502 (13502) covalent geometry : angle 0.67722 (19473) *********************** REFINEMENT MACRO_CYCLE 8 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 179 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.939 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.9433 (t80) cc_final: 0.9015 (t80) REVERT: A 74 GLU cc_start: 0.9256 (tt0) cc_final: 0.8554 (mt-10) REVERT: A 85 TYR cc_start: 0.9614 (m-80) cc_final: 0.9082 (m-80) REVERT: A 96 GLN cc_start: 0.9244 (tp-100) cc_final: 0.8870 (tp40) REVERT: A 97 GLU cc_start: 0.9497 (mt-10) cc_final: 0.9217 (mt-10) REVERT: A 137 GLN cc_start: 0.9110 (mp10) cc_final: 0.8614 (mp10) REVERT: B 49 LEU cc_start: 0.9779 (mp) cc_final: 0.9543 (mp) REVERT: B 59 LYS cc_start: 0.9747 (ptmt) cc_final: 0.9387 (ptmm) REVERT: B 63 GLU cc_start: 0.9461 (mt-10) cc_final: 0.8942 (mp0) REVERT: B 72 TYR cc_start: 0.9706 (m-80) cc_final: 0.9394 (m-80) REVERT: B 87 VAL cc_start: 0.9813 (t) cc_final: 0.9610 (t) REVERT: B 91 LYS cc_start: 0.9483 (ttpp) cc_final: 0.8975 (pttm) REVERT: C 36 LYS cc_start: 0.9529 (mtpt) cc_final: 0.8997 (mmtp) REVERT: C 95 LYS cc_start: 0.9696 (tttp) cc_final: 0.9486 (tptm) REVERT: C 102 ILE cc_start: 0.9446 (tp) cc_final: 0.8993 (tp) REVERT: D 57 LYS cc_start: 0.9483 (mmmt) cc_final: 0.9132 (mmmt) REVERT: D 95 GLN cc_start: 0.9692 (tt0) cc_final: 0.8941 (tt0) REVERT: D 99 ARG cc_start: 0.9304 (mtt180) cc_final: 0.8709 (ttm110) REVERT: E 51 GLU cc_start: 0.9635 (mm-30) cc_final: 0.9332 (mm-30) REVERT: E 85 TYR cc_start: 0.9561 (m-10) cc_final: 0.9013 (m-80) REVERT: E 97 GLU cc_start: 0.9575 (tt0) cc_final: 0.9300 (tt0) REVERT: E 128 GLN cc_start: 0.9721 (tt0) cc_final: 0.9068 (tp-100) REVERT: F 74 GLU cc_start: 0.9598 (tt0) cc_final: 0.9137 (tm-30) REVERT: G 73 ASN cc_start: 0.9398 (t0) cc_final: 0.9068 (m110) REVERT: G 95 LYS cc_start: 0.9649 (tttp) cc_final: 0.9367 (tptt) REVERT: H 59 MET cc_start: 0.8993 (tpt) cc_final: 0.8717 (tpt) REVERT: H 72 ARG cc_start: 0.9617 (ptm160) cc_final: 0.9361 (ptm160) REVERT: H 80 LEU cc_start: 0.9679 (tp) cc_final: 0.9447 (tp) REVERT: H 99 ARG cc_start: 0.9534 (mtt90) cc_final: 0.8755 (ttm110) REVERT: H 113 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8758 (tm-30) REVERT: K 661 ARG cc_start: 0.9267 (mpp-170) cc_final: 0.8879 (mpt180) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.3009 time to fit residues: 72.6768 Evaluate side-chains 144 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 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 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.022115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2287 r_free = 0.2287 target = 0.018462 restraints weight = 182241.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2321 r_free = 0.2321 target = 0.019183 restraints weight = 88516.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2345 r_free = 0.2345 target = 0.019671 restraints weight = 53387.292| |-----------------------------------------------------------------------------| r_work (final): 0.2338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 13502 Z= 0.289 Angle : 0.714 14.324 19473 Z= 0.416 Chirality : 0.041 0.162 2213 Planarity : 0.005 0.048 1473 Dihedral : 34.804 132.434 4104 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.29), residues: 838 helix: 0.87 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.53 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 87 HIS 0.010 0.001 HIS B 75 PHE 0.027 0.003 PHE E 79 TYR 0.023 0.002 TYR C 57 ARG 0.009 0.001 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.07727 ( 745) hydrogen bonds : angle 3.91852 ( 1869) covalent geometry : bond 0.00614 (13502) covalent geometry : angle 0.71363 (19473) *********************** REFINEMENT MACRO_CYCLE 9 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 173 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.998 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 74 GLU cc_start: 0.9242 (tt0) cc_final: 0.8560 (mt-10) REVERT: A 85 TYR cc_start: 0.9618 (m-80) cc_final: 0.9116 (m-80) REVERT: A 96 GLN cc_start: 0.9245 (tp-100) cc_final: 0.8865 (tp40) REVERT: A 97 GLU cc_start: 0.9521 (mt-10) cc_final: 0.9234 (mt-10) REVERT: B 59 LYS cc_start: 0.9743 (ptmt) cc_final: 0.9399 (ptmm) REVERT: B 63 GLU cc_start: 0.9476 (mt-10) cc_final: 0.8995 (mp0) REVERT: B 66 ILE cc_start: 0.9860 (mt) cc_final: 0.9580 (tt) REVERT: B 72 TYR cc_start: 0.9691 (m-80) cc_final: 0.9456 (m-80) REVERT: B 91 LYS cc_start: 0.9483 (ttpp) cc_final: 0.8979 (pttm) REVERT: C 36 LYS cc_start: 0.9525 (mtpt) cc_final: 0.8994 (mmtp) REVERT: C 95 LYS cc_start: 0.9698 (tttp) cc_final: 0.9490 (tptm) REVERT: C 102 ILE cc_start: 0.9466 (tp) cc_final: 0.8995 (tp) REVERT: D 57 LYS cc_start: 0.9476 (mmmt) cc_final: 0.9199 (mmmt) REVERT: D 95 GLN cc_start: 0.9718 (tt0) cc_final: 0.8970 (tt0) REVERT: D 99 ARG cc_start: 0.9360 (mtt180) cc_final: 0.8742 (ttm110) REVERT: E 51 GLU cc_start: 0.9619 (mm-30) cc_final: 0.9312 (mm-30) REVERT: E 85 TYR cc_start: 0.9588 (m-10) cc_final: 0.9078 (m-80) REVERT: E 97 GLU cc_start: 0.9552 (tt0) cc_final: 0.8978 (tt0) REVERT: E 128 GLN cc_start: 0.9713 (tt0) cc_final: 0.8834 (tp-100) REVERT: F 59 LYS cc_start: 0.9782 (ptmm) cc_final: 0.9500 (ptmm) REVERT: F 62 LEU cc_start: 0.9788 (pp) cc_final: 0.9473 (pp) REVERT: F 68 ASP cc_start: 0.9657 (m-30) cc_final: 0.9454 (m-30) REVERT: F 74 GLU cc_start: 0.9597 (tt0) cc_final: 0.9176 (tm-30) REVERT: G 73 ASN cc_start: 0.9442 (t0) cc_final: 0.9121 (m110) REVERT: G 95 LYS cc_start: 0.9643 (tttp) cc_final: 0.9361 (tptt) REVERT: H 59 MET cc_start: 0.9025 (tpt) cc_final: 0.8809 (tpt) REVERT: H 72 ARG cc_start: 0.9625 (ptm160) cc_final: 0.9341 (ptm160) REVERT: H 80 LEU cc_start: 0.9680 (tp) cc_final: 0.9461 (tp) REVERT: H 113 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8773 (tm-30) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.3007 time to fit residues: 71.0037 Evaluate side-chains 131 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 103 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.023293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2331 r_free = 0.2331 target = 0.019504 restraints weight = 172754.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.020272 restraints weight = 82888.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2392 r_free = 0.2392 target = 0.020790 restraints weight = 49440.342| |-----------------------------------------------------------------------------| r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13502 Z= 0.188 Angle : 0.688 13.250 19473 Z= 0.400 Chirality : 0.041 0.212 2213 Planarity : 0.005 0.045 1473 Dihedral : 34.683 131.882 4104 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.29), residues: 838 helix: 1.02 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.35 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 87 HIS 0.008 0.001 HIS B 75 PHE 0.015 0.002 PHE A 102 TYR 0.021 0.001 TYR C 57 ARG 0.018 0.001 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.05310 ( 745) hydrogen bonds : angle 3.73213 ( 1869) covalent geometry : bond 0.00401 (13502) covalent geometry : angle 0.68767 (19473) ********************** REFINEMENT MACRO_CYCLE 10 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: 0 poor density : 183 time to evaluate : 1.089 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: symmetry clash REVERT: A 74 GLU cc_start: 0.9261 (tt0) cc_final: 0.8596 (mt-10) REVERT: A 85 TYR cc_start: 0.9599 (m-80) cc_final: 0.9052 (m-80) REVERT: A 97 GLU cc_start: 0.9518 (mt-10) cc_final: 0.9085 (mt-10) REVERT: A 109 ASP cc_start: 0.9586 (m-30) cc_final: 0.9265 (m-30) REVERT: B 59 LYS cc_start: 0.9731 (ptmt) cc_final: 0.9385 (ptmm) REVERT: B 63 GLU cc_start: 0.9473 (mt-10) cc_final: 0.8936 (mp0) REVERT: B 72 TYR cc_start: 0.9696 (m-80) cc_final: 0.9392 (m-10) REVERT: B 84 MET cc_start: 0.9565 (mmp) cc_final: 0.9287 (mmp) REVERT: C 36 LYS cc_start: 0.9509 (mtpt) cc_final: 0.8969 (mmtp) REVERT: C 95 LYS cc_start: 0.9681 (tttp) cc_final: 0.9444 (tptm) REVERT: C 102 ILE cc_start: 0.9423 (tp) cc_final: 0.8955 (tp) REVERT: D 57 LYS cc_start: 0.9435 (mmmt) cc_final: 0.9099 (mmmt) REVERT: D 68 ASP cc_start: 0.9359 (t70) cc_final: 0.8926 (t0) REVERT: D 71 GLU cc_start: 0.9226 (pp20) cc_final: 0.8712 (pp20) REVERT: D 72 ARG cc_start: 0.9646 (ttm170) cc_final: 0.9183 (ptm160) REVERT: D 99 ARG cc_start: 0.9291 (mtt180) cc_final: 0.8693 (ttm110) REVERT: E 74 GLU cc_start: 0.9517 (mt-10) cc_final: 0.9182 (mt-10) REVERT: E 85 TYR cc_start: 0.9556 (m-10) cc_final: 0.8977 (m-80) REVERT: E 97 GLU cc_start: 0.9523 (tt0) cc_final: 0.8929 (tt0) REVERT: E 102 PHE cc_start: 0.9674 (t80) cc_final: 0.9282 (t80) REVERT: E 128 GLN cc_start: 0.9661 (tt0) cc_final: 0.9407 (tp40) REVERT: F 63 GLU cc_start: 0.9406 (mp0) cc_final: 0.9037 (mp0) REVERT: F 74 GLU cc_start: 0.9585 (tt0) cc_final: 0.9137 (tm-30) REVERT: F 79 LYS cc_start: 0.9086 (mtmt) cc_final: 0.8803 (ttpp) REVERT: G 56 GLU cc_start: 0.9448 (tt0) cc_final: 0.9171 (mt-10) REVERT: G 73 ASN cc_start: 0.9376 (t0) cc_final: 0.9052 (m110) REVERT: G 95 LYS cc_start: 0.9633 (tttp) cc_final: 0.9357 (tptt) REVERT: G 102 ILE cc_start: 0.8832 (tp) cc_final: 0.8610 (tp) REVERT: H 72 ARG cc_start: 0.9655 (ptm160) cc_final: 0.9371 (ptm160) REVERT: H 79 ARG cc_start: 0.9604 (ptp-110) cc_final: 0.9195 (ptp90) REVERT: H 80 LEU cc_start: 0.9656 (tp) cc_final: 0.9410 (tp) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2869 time to fit residues: 71.8635 Evaluate side-chains 139 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 109 optimal weight: 0.0170 chunk 66 optimal weight: 3.9990 chunk 103 optimal weight: 30.0000 chunk 20 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 overall best weight: 3.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 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** G 112 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.023224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2331 r_free = 0.2331 target = 0.019450 restraints weight = 172336.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2367 r_free = 0.2367 target = 0.020216 restraints weight = 81881.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.020743 restraints weight = 48642.680| |-----------------------------------------------------------------------------| r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13502 Z= 0.202 Angle : 0.682 12.962 19473 Z= 0.398 Chirality : 0.040 0.200 2213 Planarity : 0.005 0.045 1473 Dihedral : 34.575 132.013 4104 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.29), residues: 838 helix: 0.96 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.38 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 87 HIS 0.008 0.001 HIS B 75 PHE 0.022 0.002 PHE A 68 TYR 0.033 0.002 TYR H 83 ARG 0.012 0.001 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.05705 ( 745) hydrogen bonds : angle 3.77125 ( 1869) covalent geometry : bond 0.00430 (13502) covalent geometry : angle 0.68160 (19473) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3433.33 seconds wall clock time: 62 minutes 17.29 seconds (3737.29 seconds total)