Starting phenix.real_space_refine on Mon Nov 18 09:47:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqy_34954/11_2024/8hqy_34954.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqy_34954/11_2024/8hqy_34954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqy_34954/11_2024/8hqy_34954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqy_34954/11_2024/8hqy_34954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqy_34954/11_2024/8hqy_34954.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqy_34954/11_2024/8hqy_34954.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5090 atoms to isotropic. 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 272 5.49 5 S 12 5.16 5 C 6888 2.51 5 N 2298 2.21 5 O 2832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12302 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 707 Classifications: {'peptide': 91} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 87} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 707 Classifications: {'peptide': 91} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 87} Chain: "S" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "U" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 593 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "I" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2775 Classifications: {'DNA': 136} Link IDs: {'rna3p': 135} Chain: "J" Number of atoms: 2801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2801 Classifications: {'DNA': 136} Link IDs: {'rna3p': 135} Time building chain proxies: 7.26, per 1000 atoms: 0.59 Number of scatterers: 12302 At special positions: 0 Unit cell: (123.51, 102.03, 115.992, 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 272 15.00 O 2832 8.00 N 2298 7.00 C 6888 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: 2.84 Conformation dependent library (CDL) restraints added in 1.1 seconds 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1586 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 11 sheets defined 67.0% alpha, 4.2% beta 135 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 6.01 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.984A pdb=" N ARG A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.667A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.665A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.605A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.718A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.534A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.683A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.676A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.533A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 4.124A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.070A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.722A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.494A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.710A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.678A pdb=" N ILE H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.567A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG H 99 " --> pdb=" O GLN H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.749A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 34 removed outlier: 3.529A pdb=" N LYS U 33 " --> pdb=" O LYS U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.783A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.569A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.528A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.786A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.495A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'U' and resid 12 through 16 removed outlier: 3.566A pdb=" N LEU U 15 " --> pdb=" O ILE U 3 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU U 69 " --> pdb=" O LYS U 6 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 343 hydrogen bonds 670 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 4.31 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 2020 1.32 - 1.44: 4361 1.44 - 1.56: 6123 1.56 - 1.68: 542 1.68 - 1.80: 23 Bond restraints: 13069 Sorted by residual: bond pdb=" CB GLU D 113 " pdb=" CG GLU D 113 " ideal model delta sigma weight residual 1.520 1.431 0.089 3.00e-02 1.11e+03 8.86e+00 bond pdb=" CG1 ILE F 50 " pdb=" CD1 ILE F 50 " ideal model delta sigma weight residual 1.513 1.400 0.113 3.90e-02 6.57e+02 8.39e+00 bond pdb=" C HIS H 49 " pdb=" N PRO H 50 " ideal model delta sigma weight residual 1.334 1.311 0.023 8.40e-03 1.42e+04 7.48e+00 bond pdb=" CB ARG B 92 " pdb=" CG ARG B 92 " ideal model delta sigma weight residual 1.520 1.440 0.080 3.00e-02 1.11e+03 7.10e+00 bond pdb=" CG1 ILE B 50 " pdb=" CD1 ILE B 50 " ideal model delta sigma weight residual 1.513 1.416 0.097 3.90e-02 6.57e+02 6.20e+00 ... (remaining 13064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 18138 2.39 - 4.78: 616 4.78 - 7.17: 45 7.17 - 9.56: 11 9.56 - 11.95: 3 Bond angle restraints: 18813 Sorted by residual: angle pdb=" N ARG U 72 " pdb=" CA ARG U 72 " pdb=" C ARG U 72 " ideal model delta sigma weight residual 110.91 116.07 -5.16 1.17e+00 7.31e-01 1.94e+01 angle pdb=" C SER S 181 " pdb=" N ASP S 182 " pdb=" CA ASP S 182 " ideal model delta sigma weight residual 121.80 132.51 -10.71 2.44e+00 1.68e-01 1.93e+01 angle pdb=" N ILE U 23 " pdb=" CA ILE U 23 " pdb=" C ILE U 23 " ideal model delta sigma weight residual 112.96 108.79 4.17 1.00e+00 1.00e+00 1.74e+01 angle pdb=" C LEU U 69 " pdb=" N VAL U 70 " pdb=" CA VAL U 70 " ideal model delta sigma weight residual 121.97 114.98 6.99 1.80e+00 3.09e-01 1.51e+01 angle pdb=" N ASP S 182 " pdb=" CA ASP S 182 " pdb=" C ASP S 182 " ideal model delta sigma weight residual 109.81 118.16 -8.35 2.21e+00 2.05e-01 1.43e+01 ... (remaining 18808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.96: 5473 28.96 - 57.93: 1574 57.93 - 86.89: 119 86.89 - 115.85: 1 115.85 - 144.82: 3 Dihedral angle restraints: 7170 sinusoidal: 4714 harmonic: 2456 Sorted by residual: dihedral pdb=" CA ALA A 114 " pdb=" C ALA A 114 " pdb=" N LYS A 115 " pdb=" CA LYS A 115 " ideal model delta harmonic sigma weight residual 180.00 156.65 23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA LEU U 71 " pdb=" C LEU U 71 " pdb=" N ARG U 72 " pdb=" CA ARG U 72 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA VAL U 70 " pdb=" C VAL U 70 " pdb=" N LEU U 71 " pdb=" CA LEU U 71 " ideal model delta harmonic sigma weight residual 180.00 -157.73 -22.27 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 7167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1548 0.061 - 0.122: 511 0.122 - 0.183: 79 0.183 - 0.244: 10 0.244 - 0.306: 1 Chirality restraints: 2149 Sorted by residual: chirality pdb=" CG LEU E 126 " pdb=" CB LEU E 126 " pdb=" CD1 LEU E 126 " pdb=" CD2 LEU E 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ASP S 182 " pdb=" N ASP S 182 " pdb=" C ASP S 182 " pdb=" CB ASP S 182 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2146 not shown) Planarity restraints: 1438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 25 " -0.021 2.00e-02 2.50e+03 1.82e-02 5.77e+00 pdb=" CG PHE G 25 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE G 25 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE G 25 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE G 25 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE G 25 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE G 25 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 25 " -0.018 2.00e-02 2.50e+03 1.75e-02 5.38e+00 pdb=" CG PHE C 25 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE C 25 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE C 25 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 25 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 25 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 25 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 113 " -0.015 2.00e-02 2.50e+03 1.74e-02 4.53e+00 pdb=" CG HIS A 113 " 0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS A 113 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS A 113 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS A 113 " 0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS A 113 " -0.010 2.00e-02 2.50e+03 ... (remaining 1435 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2351 2.77 - 3.30: 10282 3.30 - 3.84: 24690 3.84 - 4.37: 28483 4.37 - 4.90: 40595 Nonbonded interactions: 106401 Sorted by model distance: nonbonded pdb=" O2 DC I 116 " pdb=" N2 DG J 32 " model vdw 2.238 2.496 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.264 3.040 nonbonded pdb=" N2 DG I 126 " pdb=" O2 DC J 22 " model vdw 2.274 2.496 nonbonded pdb=" O HIS D 109 " pdb=" OG SER D 112 " model vdw 2.288 3.040 nonbonded pdb=" OE1 GLN A 68 " pdb=" NH1 ARG A 72 " model vdw 2.291 3.120 ... (remaining 106396 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 13 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 32.020 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 : 0.011 0.113 13069 Z= 0.668 Angle : 1.013 11.952 18813 Z= 0.579 Chirality : 0.059 0.306 2149 Planarity : 0.007 0.052 1438 Dihedral : 27.346 144.817 5584 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.14 % Allowed : 3.24 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: -3.02 (0.24), residues: 828 helix: -1.68 (0.18), residues: 551 sheet: -3.05 (0.99), residues: 20 loop : -2.24 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP S 164 HIS 0.020 0.004 HIS A 113 PHE 0.040 0.005 PHE C 25 TYR 0.021 0.003 TYR F 98 ARG 0.017 0.002 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 306 time to evaluate : 1.236 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: B 59 LYS cc_start: 0.9107 (tptt) cc_final: 0.8691 (tptp) REVERT: B 88 TYR cc_start: 0.8837 (m-10) cc_final: 0.8138 (m-10) REVERT: C 104 GLN cc_start: 0.8399 (mm110) cc_final: 0.8064 (mm-40) REVERT: D 105 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7819 (tp30) REVERT: E 41 TYR cc_start: 0.8368 (m-80) cc_final: 0.8007 (m-10) REVERT: F 59 LYS cc_start: 0.9203 (tptm) cc_final: 0.8663 (mmmm) REVERT: F 88 TYR cc_start: 0.8962 (m-10) cc_final: 0.8478 (m-80) REVERT: G 15 LYS cc_start: 0.8776 (ttmm) cc_final: 0.8382 (tmmt) REVERT: G 112 GLN cc_start: 0.9107 (mm-40) cc_final: 0.8856 (mm110) REVERT: H 59 MET cc_start: 0.8941 (tpp) cc_final: 0.8616 (tpp) REVERT: H 83 TYR cc_start: 0.8318 (m-10) cc_final: 0.7991 (m-10) REVERT: U 48 LYS cc_start: 0.8553 (pttt) cc_final: 0.8178 (pttp) REVERT: U 50 LEU cc_start: 0.7793 (mm) cc_final: 0.7516 (mm) REVERT: U 63 LYS cc_start: 0.7992 (mttt) cc_final: 0.7710 (mtpp) REVERT: U 68 HIS cc_start: 0.8526 (m-70) cc_final: 0.8247 (m90) outliers start: 1 outliers final: 1 residues processed: 307 average time/residue: 0.3682 time to fit residues: 145.7903 Evaluate side-chains 218 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN C 104 GLN D 47 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 49 GLN U 68 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13069 Z= 0.260 Angle : 0.662 11.545 18813 Z= 0.389 Chirality : 0.039 0.237 2149 Planarity : 0.005 0.048 1438 Dihedral : 30.944 147.931 3909 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.53 % Allowed : 11.00 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: -0.52 (0.29), residues: 828 helix: 0.43 (0.21), residues: 553 sheet: -2.54 (1.04), residues: 19 loop : -1.80 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 164 HIS 0.004 0.001 HIS B 75 PHE 0.015 0.002 PHE E 67 TYR 0.031 0.001 TYR D 83 ARG 0.008 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 259 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8648 (mt-10) REVERT: A 59 GLU cc_start: 0.8632 (pm20) cc_final: 0.8418 (pm20) REVERT: A 68 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8669 (tm-30) REVERT: A 106 ASP cc_start: 0.7991 (m-30) cc_final: 0.7536 (m-30) REVERT: B 59 LYS cc_start: 0.8943 (tptt) cc_final: 0.8699 (tptp) REVERT: B 63 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7915 (mt-10) REVERT: C 57 TYR cc_start: 0.9268 (t80) cc_final: 0.8968 (t80) REVERT: C 89 ASN cc_start: 0.9192 (m-40) cc_final: 0.8930 (m-40) REVERT: D 59 MET cc_start: 0.8852 (tpp) cc_final: 0.8639 (tpt) REVERT: D 63 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8616 (m-40) REVERT: E 41 TYR cc_start: 0.8269 (m-80) cc_final: 0.8055 (m-10) REVERT: E 93 GLN cc_start: 0.8827 (tp40) cc_final: 0.8318 (tp40) REVERT: F 25 ASN cc_start: 0.9062 (OUTLIER) cc_final: 0.8354 (m-40) REVERT: F 59 LYS cc_start: 0.9264 (tptm) cc_final: 0.9018 (tptt) REVERT: G 15 LYS cc_start: 0.8637 (ttmm) cc_final: 0.8366 (tmmt) REVERT: G 56 GLU cc_start: 0.8249 (tt0) cc_final: 0.7864 (mt-10) REVERT: G 89 ASN cc_start: 0.8828 (m110) cc_final: 0.8204 (m110) REVERT: G 92 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8164 (mt-10) REVERT: G 112 GLN cc_start: 0.9120 (mm-40) cc_final: 0.8815 (mm110) REVERT: H 59 MET cc_start: 0.9066 (tpp) cc_final: 0.8744 (tpp) REVERT: H 83 TYR cc_start: 0.8270 (m-10) cc_final: 0.7954 (m-10) REVERT: H 93 GLU cc_start: 0.8516 (mp0) cc_final: 0.8180 (mp0) REVERT: S 167 ARG cc_start: 0.8427 (mtp180) cc_final: 0.8097 (mtm-85) REVERT: U 13 ILE cc_start: 0.9164 (mm) cc_final: 0.8767 (mm) REVERT: U 15 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8015 (pp) REVERT: U 29 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8737 (mptt) REVERT: U 48 LYS cc_start: 0.8525 (pttt) cc_final: 0.8137 (pttp) outliers start: 25 outliers final: 11 residues processed: 270 average time/residue: 0.2800 time to fit residues: 103.7755 Evaluate side-chains 255 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 240 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 33 optimal weight: 0.0980 chunk 78 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN F 75 HIS G 73 ASN G 104 GLN U 40 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13069 Z= 0.288 Angle : 0.638 7.219 18813 Z= 0.377 Chirality : 0.039 0.192 2149 Planarity : 0.004 0.048 1438 Dihedral : 30.718 149.380 3908 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.53 % Allowed : 14.10 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: 0.52 (0.30), residues: 828 helix: 1.31 (0.22), residues: 553 sheet: -1.84 (1.05), residues: 19 loop : -1.64 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 164 HIS 0.006 0.001 HIS B 75 PHE 0.012 0.002 PHE E 67 TYR 0.020 0.001 TYR D 83 ARG 0.004 0.001 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 245 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: A 50 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8642 (mt-10) REVERT: A 68 GLN cc_start: 0.8759 (tm130) cc_final: 0.8347 (tm-30) REVERT: B 44 LYS cc_start: 0.9157 (mtpt) cc_final: 0.8900 (mtpp) REVERT: B 59 LYS cc_start: 0.8968 (tptt) cc_final: 0.8582 (tptp) REVERT: B 63 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7857 (mt-10) REVERT: C 57 TYR cc_start: 0.9275 (t80) cc_final: 0.8951 (t80) REVERT: C 64 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8417 (tm-30) REVERT: C 89 ASN cc_start: 0.9244 (m-40) cc_final: 0.8880 (m110) REVERT: D 63 ASN cc_start: 0.8881 (OUTLIER) cc_final: 0.8673 (m110) REVERT: E 41 TYR cc_start: 0.8270 (m-80) cc_final: 0.8036 (m-10) REVERT: E 79 LYS cc_start: 0.8713 (tptp) cc_final: 0.8460 (tptp) REVERT: E 93 GLN cc_start: 0.8917 (tp40) cc_final: 0.8296 (tp40) REVERT: E 120 MET cc_start: 0.8431 (mmm) cc_final: 0.8229 (mmm) REVERT: F 25 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8366 (m-40) REVERT: G 15 LYS cc_start: 0.8707 (ttmm) cc_final: 0.8380 (tmmt) REVERT: G 89 ASN cc_start: 0.8920 (m110) cc_final: 0.8278 (m110) REVERT: G 92 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8177 (mt-10) REVERT: G 112 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8792 (mm110) REVERT: H 93 GLU cc_start: 0.8568 (mp0) cc_final: 0.8233 (mp0) REVERT: U 13 ILE cc_start: 0.9067 (mm) cc_final: 0.8529 (mm) REVERT: U 15 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8117 (pp) REVERT: U 29 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8747 (mptt) REVERT: U 50 LEU cc_start: 0.8657 (mm) cc_final: 0.7808 (mm) outliers start: 25 outliers final: 14 residues processed: 254 average time/residue: 0.2772 time to fit residues: 96.8134 Evaluate side-chains 252 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 235 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN C 112 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13069 Z= 0.299 Angle : 0.640 7.201 18813 Z= 0.375 Chirality : 0.039 0.196 2149 Planarity : 0.004 0.050 1438 Dihedral : 30.575 149.078 3908 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.37 % Allowed : 16.22 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: 0.92 (0.30), residues: 828 helix: 1.70 (0.22), residues: 550 sheet: -2.06 (1.06), residues: 19 loop : -1.61 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP S 164 HIS 0.006 0.001 HIS B 75 PHE 0.011 0.002 PHE E 67 TYR 0.015 0.001 TYR H 83 ARG 0.003 0.001 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 1.034 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: A 50 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8647 (mt-10) REVERT: A 62 ILE cc_start: 0.9426 (mp) cc_final: 0.8388 (mp) REVERT: A 68 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8385 (tm-30) REVERT: A 106 ASP cc_start: 0.8112 (m-30) cc_final: 0.7820 (m-30) REVERT: B 44 LYS cc_start: 0.9311 (mtpt) cc_final: 0.9022 (mtpp) REVERT: B 59 LYS cc_start: 0.9021 (tptt) cc_final: 0.8563 (tptp) REVERT: B 63 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7896 (mt-10) REVERT: C 57 TYR cc_start: 0.9255 (t80) cc_final: 0.8991 (t80) REVERT: C 89 ASN cc_start: 0.9275 (m-40) cc_final: 0.8993 (m-40) REVERT: D 63 ASN cc_start: 0.8874 (OUTLIER) cc_final: 0.8646 (m110) REVERT: E 41 TYR cc_start: 0.8280 (m-80) cc_final: 0.8063 (m-10) REVERT: E 93 GLN cc_start: 0.8962 (tp40) cc_final: 0.8306 (tp40) REVERT: F 25 ASN cc_start: 0.8972 (OUTLIER) cc_final: 0.8259 (m-40) REVERT: F 88 TYR cc_start: 0.8930 (m-10) cc_final: 0.8314 (m-80) REVERT: G 15 LYS cc_start: 0.8624 (ttmm) cc_final: 0.8349 (tmmt) REVERT: G 56 GLU cc_start: 0.8275 (tt0) cc_final: 0.7822 (mt-10) REVERT: H 83 TYR cc_start: 0.8236 (m-10) cc_final: 0.7972 (m-10) REVERT: H 93 GLU cc_start: 0.8561 (mp0) cc_final: 0.8225 (mp0) REVERT: S 175 VAL cc_start: 0.9108 (t) cc_final: 0.8829 (p) REVERT: U 11 LYS cc_start: 0.8966 (ttpt) cc_final: 0.8741 (ttpp) REVERT: U 13 ILE cc_start: 0.9084 (mm) cc_final: 0.8858 (mm) REVERT: U 15 LEU cc_start: 0.8486 (pp) cc_final: 0.8230 (pp) REVERT: U 29 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8752 (mptt) outliers start: 31 outliers final: 18 residues processed: 250 average time/residue: 0.2885 time to fit residues: 98.4663 Evaluate side-chains 248 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 227 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN C 112 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13069 Z= 0.318 Angle : 0.650 9.668 18813 Z= 0.378 Chirality : 0.039 0.195 2149 Planarity : 0.004 0.052 1438 Dihedral : 30.536 149.256 3908 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.94 % Allowed : 15.66 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: 1.14 (0.30), residues: 828 helix: 1.85 (0.22), residues: 553 sheet: -1.96 (1.05), residues: 19 loop : -1.53 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP S 164 HIS 0.005 0.001 HIS B 75 PHE 0.012 0.002 PHE D 65 TYR 0.014 0.001 TYR G 57 ARG 0.004 0.001 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 227 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8645 (mt-10) REVERT: A 68 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8393 (tm-30) REVERT: A 106 ASP cc_start: 0.8086 (m-30) cc_final: 0.7802 (m-30) REVERT: B 59 LYS cc_start: 0.9031 (tptt) cc_final: 0.8766 (tptp) REVERT: B 63 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8004 (mt-10) REVERT: C 57 TYR cc_start: 0.9261 (t80) cc_final: 0.9027 (t80) REVERT: C 89 ASN cc_start: 0.9285 (m-40) cc_final: 0.9018 (m-40) REVERT: D 68 ASP cc_start: 0.8819 (t70) cc_final: 0.8457 (t0) REVERT: D 116 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.9059 (ttpp) REVERT: E 93 GLN cc_start: 0.8978 (tp40) cc_final: 0.8232 (tp40) REVERT: F 25 ASN cc_start: 0.8966 (OUTLIER) cc_final: 0.8555 (m-40) REVERT: F 74 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8244 (mm-30) REVERT: G 15 LYS cc_start: 0.8673 (ttmm) cc_final: 0.8374 (tmmt) REVERT: G 56 GLU cc_start: 0.8230 (tt0) cc_final: 0.7774 (mt-10) REVERT: G 92 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8223 (mt-10) REVERT: H 83 TYR cc_start: 0.8274 (m-10) cc_final: 0.7941 (m-10) REVERT: H 93 GLU cc_start: 0.8594 (mp0) cc_final: 0.8216 (mp0) REVERT: S 175 VAL cc_start: 0.9136 (t) cc_final: 0.8875 (p) REVERT: U 11 LYS cc_start: 0.8979 (ttpt) cc_final: 0.8663 (ptmm) REVERT: U 29 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8780 (mptt) outliers start: 35 outliers final: 22 residues processed: 243 average time/residue: 0.3022 time to fit residues: 100.0544 Evaluate side-chains 247 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 60 ASN Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 63 ASN D 95 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13069 Z= 0.199 Angle : 0.612 7.460 18813 Z= 0.359 Chirality : 0.036 0.158 2149 Planarity : 0.004 0.051 1438 Dihedral : 30.250 147.808 3908 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.53 % Allowed : 17.63 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: 1.53 (0.31), residues: 828 helix: 2.17 (0.22), residues: 553 sheet: -2.13 (0.99), residues: 19 loop : -1.39 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP S 164 HIS 0.003 0.001 HIS B 75 PHE 0.015 0.001 PHE D 65 TYR 0.012 0.001 TYR G 57 ARG 0.003 0.000 ARG U 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 251 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8611 (mt-10) REVERT: A 79 LYS cc_start: 0.8580 (tptp) cc_final: 0.8346 (tptp) REVERT: A 106 ASP cc_start: 0.8069 (m-30) cc_final: 0.7834 (m-30) REVERT: B 44 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8899 (mtpp) REVERT: B 59 LYS cc_start: 0.9016 (tptt) cc_final: 0.8470 (tptp) REVERT: B 63 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7890 (mt-10) REVERT: C 57 TYR cc_start: 0.9191 (t80) cc_final: 0.8965 (t80) REVERT: D 68 ASP cc_start: 0.8738 (t70) cc_final: 0.8424 (t0) REVERT: E 79 LYS cc_start: 0.8592 (tptm) cc_final: 0.8285 (tptp) REVERT: E 93 GLN cc_start: 0.8883 (tp40) cc_final: 0.8364 (tp40) REVERT: F 25 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8548 (m-40) REVERT: F 74 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8252 (mm-30) REVERT: F 88 TYR cc_start: 0.8898 (m-10) cc_final: 0.8085 (m-10) REVERT: G 15 LYS cc_start: 0.8625 (ttmm) cc_final: 0.8259 (tmmt) REVERT: G 56 GLU cc_start: 0.8249 (tt0) cc_final: 0.7825 (mt-10) REVERT: G 89 ASN cc_start: 0.8934 (m110) cc_final: 0.8256 (m110) REVERT: H 93 GLU cc_start: 0.8545 (mp0) cc_final: 0.8222 (mp0) REVERT: H 105 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7741 (tp30) REVERT: S 175 VAL cc_start: 0.9046 (t) cc_final: 0.8758 (p) REVERT: U 29 LYS cc_start: 0.8861 (mmmm) cc_final: 0.8650 (mptt) REVERT: U 49 GLN cc_start: 0.8579 (tt0) cc_final: 0.8307 (tp-100) outliers start: 25 outliers final: 11 residues processed: 261 average time/residue: 0.2850 time to fit residues: 100.5204 Evaluate side-chains 245 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 233 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain S residue 176 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13069 Z= 0.246 Angle : 0.632 7.009 18813 Z= 0.368 Chirality : 0.037 0.164 2149 Planarity : 0.005 0.076 1438 Dihedral : 30.304 147.171 3908 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.24 % Allowed : 18.62 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: 1.58 (0.31), residues: 828 helix: 2.20 (0.22), residues: 549 sheet: -2.03 (0.97), residues: 19 loop : -1.29 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP S 164 HIS 0.003 0.001 HIS B 75 PHE 0.015 0.001 PHE D 65 TYR 0.038 0.002 TYR H 83 ARG 0.014 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 238 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8605 (mt-10) REVERT: B 44 LYS cc_start: 0.9193 (mtpt) cc_final: 0.8924 (mtpp) REVERT: B 59 LYS cc_start: 0.9028 (tptt) cc_final: 0.8674 (tptp) REVERT: B 63 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8050 (mt-10) REVERT: C 57 TYR cc_start: 0.9232 (t80) cc_final: 0.9030 (t80) REVERT: C 89 ASN cc_start: 0.9154 (m-40) cc_final: 0.8890 (m110) REVERT: D 68 ASP cc_start: 0.8783 (t70) cc_final: 0.8448 (t0) REVERT: E 93 GLN cc_start: 0.9064 (tp40) cc_final: 0.8400 (tp40) REVERT: F 25 ASN cc_start: 0.8962 (OUTLIER) cc_final: 0.8598 (t0) REVERT: F 88 TYR cc_start: 0.8810 (m-10) cc_final: 0.8209 (m-10) REVERT: G 15 LYS cc_start: 0.8634 (ttmm) cc_final: 0.8356 (tmmt) REVERT: G 56 GLU cc_start: 0.8296 (tt0) cc_final: 0.7870 (mt-10) REVERT: G 89 ASN cc_start: 0.8973 (m110) cc_final: 0.8289 (m110) REVERT: H 83 TYR cc_start: 0.8143 (m-10) cc_final: 0.7916 (m-80) REVERT: H 93 GLU cc_start: 0.8575 (mp0) cc_final: 0.8228 (mp0) REVERT: H 105 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7746 (tp30) REVERT: S 175 VAL cc_start: 0.8990 (t) cc_final: 0.8728 (p) REVERT: U 11 LYS cc_start: 0.9026 (ttpt) cc_final: 0.8745 (ptmm) REVERT: U 49 GLN cc_start: 0.8541 (tt0) cc_final: 0.8299 (tp-100) REVERT: U 64 GLU cc_start: 0.7076 (mp0) cc_final: 0.6707 (pm20) outliers start: 23 outliers final: 14 residues processed: 249 average time/residue: 0.2793 time to fit residues: 95.6303 Evaluate side-chains 248 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 233 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain U residue 40 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 ASN U 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13069 Z= 0.208 Angle : 0.622 7.063 18813 Z= 0.363 Chirality : 0.036 0.170 2149 Planarity : 0.004 0.055 1438 Dihedral : 30.172 146.041 3908 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.54 % Allowed : 19.61 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: 1.59 (0.31), residues: 828 helix: 2.17 (0.22), residues: 553 sheet: -1.88 (0.96), residues: 19 loop : -1.28 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP S 164 HIS 0.003 0.001 HIS B 75 PHE 0.017 0.001 PHE D 65 TYR 0.029 0.001 TYR H 83 ARG 0.013 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 244 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8592 (mt-10) REVERT: B 44 LYS cc_start: 0.9125 (mtpt) cc_final: 0.8877 (mtpp) REVERT: B 59 LYS cc_start: 0.9055 (tptt) cc_final: 0.8638 (tptp) REVERT: B 63 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8044 (mt-10) REVERT: C 64 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8296 (tm-30) REVERT: C 89 ASN cc_start: 0.9128 (m-40) cc_final: 0.8848 (m110) REVERT: D 46 LYS cc_start: 0.9163 (mmmt) cc_final: 0.8874 (mmmt) REVERT: D 68 ASP cc_start: 0.8752 (t70) cc_final: 0.8401 (t0) REVERT: E 93 GLN cc_start: 0.9033 (tp40) cc_final: 0.8396 (tp40) REVERT: F 25 ASN cc_start: 0.8959 (OUTLIER) cc_final: 0.8596 (t0) REVERT: F 88 TYR cc_start: 0.8810 (m-10) cc_final: 0.7908 (m-10) REVERT: G 15 LYS cc_start: 0.8619 (ttmm) cc_final: 0.8282 (tmmt) REVERT: G 56 GLU cc_start: 0.8227 (tt0) cc_final: 0.7804 (mt-10) REVERT: G 89 ASN cc_start: 0.8961 (m110) cc_final: 0.8323 (m110) REVERT: H 42 TYR cc_start: 0.7482 (t80) cc_final: 0.7256 (t80) REVERT: H 83 TYR cc_start: 0.8122 (m-10) cc_final: 0.7871 (m-80) REVERT: H 93 GLU cc_start: 0.8558 (mp0) cc_final: 0.8280 (mp0) REVERT: H 105 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7699 (tp30) REVERT: S 167 ARG cc_start: 0.8269 (mtp180) cc_final: 0.8029 (mtm-85) REVERT: S 175 VAL cc_start: 0.8914 (t) cc_final: 0.8585 (p) REVERT: U 11 LYS cc_start: 0.8929 (ttpt) cc_final: 0.8595 (tmmt) outliers start: 18 outliers final: 11 residues processed: 253 average time/residue: 0.2932 time to fit residues: 100.8061 Evaluate side-chains 241 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 229 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain U residue 40 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 13069 Z= 0.397 Angle : 0.707 6.955 18813 Z= 0.403 Chirality : 0.041 0.172 2149 Planarity : 0.005 0.071 1438 Dihedral : 30.566 146.345 3908 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.69 % Allowed : 20.73 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: 1.25 (0.30), residues: 828 helix: 1.91 (0.22), residues: 552 sheet: -2.09 (0.98), residues: 19 loop : -1.41 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP S 164 HIS 0.003 0.001 HIS D 49 PHE 0.014 0.002 PHE D 65 TYR 0.037 0.002 TYR H 83 ARG 0.012 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 220 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8632 (mt-10) REVERT: B 44 LYS cc_start: 0.9282 (mtpt) cc_final: 0.9001 (mtpt) REVERT: B 59 LYS cc_start: 0.9097 (tptt) cc_final: 0.8618 (tptp) REVERT: B 63 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8000 (mt-10) REVERT: C 89 ASN cc_start: 0.9196 (m-40) cc_final: 0.8877 (m110) REVERT: D 46 LYS cc_start: 0.9162 (mmmt) cc_final: 0.8865 (mmmt) REVERT: D 68 ASP cc_start: 0.8835 (t70) cc_final: 0.8493 (t0) REVERT: F 25 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.8640 (t0) REVERT: F 88 TYR cc_start: 0.8974 (m-10) cc_final: 0.8062 (m-80) REVERT: G 15 LYS cc_start: 0.8701 (ttmm) cc_final: 0.8268 (tmmt) REVERT: G 56 GLU cc_start: 0.8228 (tt0) cc_final: 0.7804 (mt-10) REVERT: H 83 TYR cc_start: 0.8145 (m-10) cc_final: 0.7935 (m-80) REVERT: U 6 LYS cc_start: 0.9149 (ttmt) cc_final: 0.8859 (mttp) REVERT: U 64 GLU cc_start: 0.7362 (mp0) cc_final: 0.7071 (mp0) outliers start: 12 outliers final: 9 residues processed: 229 average time/residue: 0.3089 time to fit residues: 95.5659 Evaluate side-chains 226 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 216 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain U residue 40 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13069 Z= 0.222 Angle : 0.648 7.362 18813 Z= 0.374 Chirality : 0.037 0.165 2149 Planarity : 0.004 0.055 1438 Dihedral : 30.266 145.416 3908 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.27 % Allowed : 21.02 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: 1.45 (0.30), residues: 828 helix: 2.05 (0.22), residues: 553 sheet: -2.11 (0.94), residues: 19 loop : -1.30 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP S 164 HIS 0.002 0.001 HIS B 75 PHE 0.019 0.001 PHE D 65 TYR 0.029 0.002 TYR H 83 ARG 0.011 0.000 ARG B 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 231 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8597 (mt-10) REVERT: B 44 LYS cc_start: 0.9174 (mtpt) cc_final: 0.8974 (mtpt) REVERT: B 59 LYS cc_start: 0.9072 (tptt) cc_final: 0.8596 (tptp) REVERT: B 63 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8035 (mt-10) REVERT: C 64 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8374 (tm-30) REVERT: C 89 ASN cc_start: 0.9179 (m-40) cc_final: 0.8811 (m110) REVERT: D 46 LYS cc_start: 0.9105 (mmmt) cc_final: 0.8853 (mmmt) REVERT: D 68 ASP cc_start: 0.8753 (t70) cc_final: 0.8408 (t0) REVERT: E 93 GLN cc_start: 0.9048 (tp40) cc_final: 0.8397 (tp40) REVERT: F 25 ASN cc_start: 0.8959 (OUTLIER) cc_final: 0.8570 (m-40) REVERT: G 15 LYS cc_start: 0.8671 (ttmm) cc_final: 0.8315 (tmmt) REVERT: G 56 GLU cc_start: 0.8279 (tt0) cc_final: 0.7857 (mt-10) REVERT: G 89 ASN cc_start: 0.8991 (m110) cc_final: 0.8315 (m110) REVERT: H 83 TYR cc_start: 0.8066 (m-10) cc_final: 0.7827 (m-80) REVERT: H 93 GLU cc_start: 0.8514 (mp0) cc_final: 0.8159 (mp0) REVERT: H 105 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7726 (tp30) REVERT: U 50 LEU cc_start: 0.8733 (mm) cc_final: 0.8527 (mm) REVERT: U 64 GLU cc_start: 0.7397 (mp0) cc_final: 0.7055 (mp0) outliers start: 9 outliers final: 7 residues processed: 238 average time/residue: 0.3269 time to fit residues: 105.5873 Evaluate side-chains 232 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 224 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 74 optimal weight: 0.0970 chunk 4 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 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 = 0.3481 r_free = 0.3481 target = 0.060351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.038973 restraints weight = 53349.061| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.39 r_work: 0.2609 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13069 Z= 0.241 Angle : 0.657 7.459 18813 Z= 0.378 Chirality : 0.037 0.167 2149 Planarity : 0.004 0.052 1438 Dihedral : 30.265 145.602 3908 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.27 % Allowed : 22.14 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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: 1.44 (0.30), residues: 828 helix: 2.05 (0.22), residues: 553 sheet: -2.18 (0.91), residues: 19 loop : -1.29 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP S 164 HIS 0.002 0.001 HIS B 75 PHE 0.018 0.001 PHE D 65 TYR 0.032 0.002 TYR H 83 ARG 0.007 0.000 ARG D 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2827.64 seconds wall clock time: 52 minutes 43.55 seconds (3163.55 seconds total)