Starting phenix.real_space_refine on Fri Mar 14 04:46:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p3q_13182/03_2025/7p3q_13182_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p3q_13182/03_2025/7p3q_13182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p3q_13182/03_2025/7p3q_13182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p3q_13182/03_2025/7p3q_13182.map" model { file = "/net/cci-nas-00/data/ceres_data/7p3q_13182/03_2025/7p3q_13182_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p3q_13182/03_2025/7p3q_13182_neut.cif" } resolution = 3.12 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= 0.083 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: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 48 5.49 5 S 64 5.16 5 C 5756 2.51 5 N 1808 2.21 5 O 1948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9632 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1145 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "B" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1139 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 140} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {' ZN': 1, 'ATP': 1, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {' ZN': 1, 'ATP': 1, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24 SG CYS A 3 46.349 87.581 52.926 1.00 65.22 S ATOM 48 SG CYS A 6 46.500 91.393 52.216 1.00 66.49 S ATOM 254 SG CYS A 31 43.952 90.097 54.511 1.00 64.58 S ATOM 275 SG CYS A 34 43.720 89.269 50.772 1.00 65.50 S ATOM 4604 SG CYS B 3 50.768 31.995 13.583 1.00107.26 S ATOM 4628 SG CYS B 6 47.797 33.059 11.728 1.00108.81 S ATOM 4834 SG CYS B 31 49.782 29.863 10.657 1.00111.23 S ATOM 4855 SG CYS B 34 51.105 33.063 9.751 1.00113.83 S Restraints were copied for chains: D, F, H, C, E, G Time building chain proxies: 4.33, per 1000 atoms: 0.45 Number of scatterers: 9632 At special positions: 0 Unit cell: (85.05, 101.43, 92.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 64 16.00 P 48 15.00 O 1948 8.00 N 1808 7.00 C 5756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 44 " distance=0.00 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 71 " distance=0.00 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: 2.33 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 203 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 6 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 31 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 34 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 3 " pdb=" ZN B 203 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 31 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 6 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 3 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 34 " pdb=" ZN C 203 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 6 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 31 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 34 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 3 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 31 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 6 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 3 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 34 " pdb=" ZN E 203 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 6 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 31 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 34 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 3 " pdb=" ZN F 203 " pdb="ZN ZN F 203 " - pdb=" SG CYS F 31 " pdb="ZN ZN F 203 " - pdb=" SG CYS F 6 " pdb="ZN ZN F 203 " - pdb=" SG CYS F 3 " pdb="ZN ZN F 203 " - pdb=" SG CYS F 34 " pdb=" ZN G 203 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 6 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 31 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 34 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 3 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 31 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 6 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 3 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 34 " Number of angles added : 48 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 53.1% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 59 through 71 removed outlier: 3.921A pdb=" N VAL A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 96 removed outlier: 3.840A pdb=" N GLY A 96 " --> pdb=" O VAL A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 117 removed outlier: 3.584A pdb=" N GLY A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Proline residue: A 112 - end of helix removed outlier: 3.788A pdb=" N GLU A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 133 through 147 removed outlier: 3.765A pdb=" N PHE A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 71 removed outlier: 3.921A pdb=" N VAL C 63 " --> pdb=" O SER C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 96 removed outlier: 3.840A pdb=" N GLY C 96 " --> pdb=" O VAL C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 117 removed outlier: 3.584A pdb=" N GLY C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Proline residue: C 112 - end of helix removed outlier: 3.787A pdb=" N GLU C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 133 through 147 removed outlier: 3.764A pdb=" N PHE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 147 " --> pdb=" O GLU C 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.922A pdb=" N VAL E 63 " --> pdb=" O SER E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 96 removed outlier: 3.840A pdb=" N GLY E 96 " --> pdb=" O VAL E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 117 removed outlier: 3.584A pdb=" N GLY E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Proline residue: E 112 - end of helix removed outlier: 3.788A pdb=" N GLU E 115 " --> pdb=" O GLY E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 133 through 147 removed outlier: 3.765A pdb=" N PHE E 137 " --> pdb=" O SER E 133 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 71 removed outlier: 3.921A pdb=" N VAL G 63 " --> pdb=" O SER G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 96 removed outlier: 3.839A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 117 removed outlier: 3.584A pdb=" N GLY G 111 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Proline residue: G 112 - end of helix removed outlier: 3.788A pdb=" N GLU G 115 " --> pdb=" O GLY G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 133 through 147 removed outlier: 3.764A pdb=" N PHE G 137 " --> pdb=" O SER G 133 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR G 147 " --> pdb=" O GLU G 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 59 through 71 removed outlier: 3.660A pdb=" N VAL B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 96 removed outlier: 3.845A pdb=" N GLY B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 117 Proline residue: B 112 - end of helix removed outlier: 4.538A pdb=" N GLU B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 59 through 71 removed outlier: 3.659A pdb=" N VAL D 63 " --> pdb=" O SER D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 96 removed outlier: 3.846A pdb=" N GLY D 96 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 117 Proline residue: D 112 - end of helix removed outlier: 4.538A pdb=" N GLU D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 133 through 146 Processing helix chain 'F' and resid 20 through 22 No H-bonds generated for 'chain 'F' and resid 20 through 22' Processing helix chain 'F' and resid 59 through 71 removed outlier: 3.660A pdb=" N VAL F 63 " --> pdb=" O SER F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 96 removed outlier: 3.845A pdb=" N GLY F 96 " --> pdb=" O VAL F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 117 Proline residue: F 112 - end of helix removed outlier: 4.538A pdb=" N GLU F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 130 Processing helix chain 'F' and resid 133 through 146 Processing helix chain 'H' and resid 20 through 22 No H-bonds generated for 'chain 'H' and resid 20 through 22' Processing helix chain 'H' and resid 59 through 71 removed outlier: 3.660A pdb=" N VAL H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 96 removed outlier: 3.846A pdb=" N GLY H 96 " --> pdb=" O VAL H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 117 Proline residue: H 112 - end of helix removed outlier: 4.538A pdb=" N GLU H 115 " --> pdb=" O GLY H 111 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 133 through 146 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 5.441A pdb=" N VAL A 13 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN A 30 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL D 41 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN D 30 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL D 13 " --> pdb=" O GLN D 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 57 Processing sheet with id=AA3, first strand: chain 'C' and resid 12 through 18 removed outlier: 5.441A pdb=" N VAL C 13 " --> pdb=" O GLN C 30 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN C 30 " --> pdb=" O VAL C 13 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B 41 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLN B 30 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL B 13 " --> pdb=" O GLN B 30 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 55 through 57 Processing sheet with id=AA5, first strand: chain 'E' and resid 12 through 18 removed outlier: 5.441A pdb=" N VAL E 13 " --> pdb=" O GLN E 30 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN E 30 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLN H 30 " --> pdb=" O VAL H 13 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL H 13 " --> pdb=" O GLN H 30 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 55 through 57 Processing sheet with id=AA7, first strand: chain 'G' and resid 12 through 18 removed outlier: 5.441A pdb=" N VAL G 13 " --> pdb=" O GLN G 30 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN G 30 " --> pdb=" O VAL G 13 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 41 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLN F 30 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL F 13 " --> pdb=" O GLN F 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 55 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 55 through 57 removed outlier: 6.397A pdb=" N MET B 47 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 55 through 57 removed outlier: 6.396A pdb=" N MET D 47 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 55 through 57 removed outlier: 6.397A pdb=" N MET F 47 " --> pdb=" O LEU F 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 55 through 57 removed outlier: 6.397A pdb=" N MET H 47 " --> pdb=" O LEU H 100 " (cutoff:3.500A) 506 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1745 1.32 - 1.45: 2424 1.45 - 1.57: 5455 1.57 - 1.70: 80 1.70 - 1.82: 80 Bond restraints: 9784 Sorted by residual: bond pdb=" CA SER A 126 " pdb=" CB SER A 126 " ideal model delta sigma weight residual 1.528 1.455 0.074 1.59e-02 3.96e+03 2.15e+01 bond pdb=" CA SER E 126 " pdb=" CB SER E 126 " ideal model delta sigma weight residual 1.528 1.455 0.074 1.59e-02 3.96e+03 2.14e+01 bond pdb=" CA SER C 126 " pdb=" CB SER C 126 " ideal model delta sigma weight residual 1.528 1.455 0.074 1.59e-02 3.96e+03 2.14e+01 bond pdb=" CA SER G 126 " pdb=" CB SER G 126 " ideal model delta sigma weight residual 1.528 1.455 0.073 1.59e-02 3.96e+03 2.12e+01 bond pdb=" N GLY D 111 " pdb=" CA GLY D 111 " ideal model delta sigma weight residual 1.444 1.483 -0.040 8.80e-03 1.29e+04 2.02e+01 ... (remaining 9779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 11470 1.76 - 3.53: 1448 3.53 - 5.29: 298 5.29 - 7.05: 91 7.05 - 8.81: 29 Bond angle restraints: 13336 Sorted by residual: angle pdb=" N ASP G 21 " pdb=" CA ASP G 21 " pdb=" C ASP G 21 " ideal model delta sigma weight residual 113.41 104.60 8.81 1.22e+00 6.72e-01 5.22e+01 angle pdb=" N ASP C 21 " pdb=" CA ASP C 21 " pdb=" C ASP C 21 " ideal model delta sigma weight residual 113.41 104.61 8.80 1.22e+00 6.72e-01 5.20e+01 angle pdb=" N ASP A 21 " pdb=" CA ASP A 21 " pdb=" C ASP A 21 " ideal model delta sigma weight residual 113.41 104.62 8.79 1.22e+00 6.72e-01 5.19e+01 angle pdb=" N ASP E 21 " pdb=" CA ASP E 21 " pdb=" C ASP E 21 " ideal model delta sigma weight residual 113.41 104.65 8.76 1.22e+00 6.72e-01 5.15e+01 angle pdb=" C5' DTP E 202 " pdb=" O5' DTP E 202 " pdb=" PA DTP E 202 " ideal model delta sigma weight residual 121.27 127.74 -6.47 1.00e+00 1.00e+00 4.18e+01 ... (remaining 13331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 5244 16.82 - 33.64: 672 33.64 - 50.45: 200 50.45 - 67.27: 88 67.27 - 84.09: 48 Dihedral angle restraints: 6252 sinusoidal: 2844 harmonic: 3408 Sorted by residual: dihedral pdb=" CB CYS C 44 " pdb=" SG CYS C 44 " pdb=" SG CYS C 44 " pdb=" CB CYS C 44 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CB CYS C 71 " pdb=" SG CYS C 71 " pdb=" SG CYS C 71 " pdb=" CB CYS C 71 " ideal model delta sinusoidal sigma weight residual 73.28 39.18 34.10 1 1.00e+01 1.00e-02 1.65e+01 dihedral pdb=" C THR A 43 " pdb=" N THR A 43 " pdb=" CA THR A 43 " pdb=" CB THR A 43 " ideal model delta harmonic sigma weight residual -122.00 -113.69 -8.31 0 2.50e+00 1.60e-01 1.11e+01 ... (remaining 6249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1028 0.056 - 0.113: 318 0.113 - 0.169: 95 0.169 - 0.226: 51 0.226 - 0.282: 16 Chirality restraints: 1508 Sorted by residual: chirality pdb=" CA ILE E 25 " pdb=" N ILE E 25 " pdb=" C ILE E 25 " pdb=" CB ILE E 25 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ILE C 25 " pdb=" N ILE C 25 " pdb=" C ILE C 25 " pdb=" CB ILE C 25 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ILE A 25 " pdb=" N ILE A 25 " pdb=" C ILE A 25 " pdb=" CB ILE A 25 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1505 not shown) Planarity restraints: 1676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 1 " -0.024 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C MET A 1 " 0.087 2.00e-02 2.50e+03 pdb=" O MET A 1 " -0.034 2.00e-02 2.50e+03 pdb=" N HIS A 2 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 1 " 0.024 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C MET C 1 " -0.087 2.00e-02 2.50e+03 pdb=" O MET C 1 " 0.034 2.00e-02 2.50e+03 pdb=" N HIS C 2 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 1 " -0.024 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C MET G 1 " 0.087 2.00e-02 2.50e+03 pdb=" O MET G 1 " -0.034 2.00e-02 2.50e+03 pdb=" N HIS G 2 " -0.029 2.00e-02 2.50e+03 ... (remaining 1673 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1229 2.75 - 3.29: 9768 3.29 - 3.83: 16651 3.83 - 4.36: 20979 4.36 - 4.90: 34206 Nonbonded interactions: 82833 Sorted by model distance: nonbonded pdb=" NH1 ARG D 26 " pdb=" OG1 THR D 39 " model vdw 2.218 3.120 nonbonded pdb=" NH1 ARG B 26 " pdb=" OG1 THR B 39 " model vdw 2.218 3.120 nonbonded pdb=" NH1 ARG H 26 " pdb=" OG1 THR H 39 " model vdw 2.218 3.120 nonbonded pdb=" NH1 ARG F 26 " pdb=" OG1 THR F 39 " model vdw 2.219 3.120 nonbonded pdb=" OG1 THR A 40 " pdb=" OE2 GLU D 42 " model vdw 2.309 3.040 ... (remaining 82828 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: 0.07 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.480 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 : 0.009 0.074 9784 Z= 0.585 Angle : 1.342 8.814 13336 Z= 0.968 Chirality : 0.070 0.282 1508 Planarity : 0.008 0.052 1676 Dihedral : 18.914 84.088 4024 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.40 % Allowed : 5.20 % Favored : 94.40 % 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 (0.26), residues: 1160 helix: 1.46 (0.23), residues: 556 sheet: 0.04 (0.35), residues: 184 loop : -1.16 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 2 PHE 0.027 0.004 PHE G 124 TYR 0.015 0.004 TYR E 121 ARG 0.006 0.001 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 205 time to evaluate : 1.547 Fit side-chains revert: symmetry clash REVERT: A 43 THR cc_start: 0.7984 (m) cc_final: 0.7534 (p) REVERT: E 43 THR cc_start: 0.7774 (m) cc_final: 0.7374 (p) outliers start: 4 outliers final: 0 residues processed: 207 average time/residue: 0.2594 time to fit residues: 70.9915 Evaluate side-chains 176 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.199004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.153335 restraints weight = 9437.277| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.09 r_work: 0.3490 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9784 Z= 0.219 Angle : 0.580 5.925 13336 Z= 0.305 Chirality : 0.039 0.129 1508 Planarity : 0.006 0.066 1676 Dihedral : 18.780 87.490 1840 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.80 % Allowed : 13.10 % Favored : 86.10 % 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: 1.19 (0.25), residues: 1160 helix: 2.12 (0.22), residues: 556 sheet: 0.41 (0.35), residues: 168 loop : -0.83 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS A 2 PHE 0.011 0.002 PHE H 38 TYR 0.010 0.002 TYR E 121 ARG 0.009 0.001 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7473 (ttm170) cc_final: 0.6752 (tmt170) REVERT: A 43 THR cc_start: 0.8266 (m) cc_final: 0.7847 (p) REVERT: C 42 GLU cc_start: 0.7771 (tt0) cc_final: 0.7472 (pt0) REVERT: C 115 GLU cc_start: 0.7890 (mp0) cc_final: 0.7573 (mp0) REVERT: G 43 THR cc_start: 0.7861 (m) cc_final: 0.7588 (p) REVERT: D 26 ARG cc_start: 0.7541 (mmm160) cc_final: 0.7320 (mmm160) REVERT: F 26 ARG cc_start: 0.7378 (mmm160) cc_final: 0.7159 (mmm160) outliers start: 8 outliers final: 7 residues processed: 178 average time/residue: 0.2582 time to fit residues: 60.9564 Evaluate side-chains 167 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 160 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 134 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN G 30 GLN ** G 114 GLN ** 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 = 0.4058 r_free = 0.4058 target = 0.187710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.140291 restraints weight = 9596.299| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.01 r_work: 0.3317 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 9784 Z= 0.442 Angle : 0.641 6.384 13336 Z= 0.332 Chirality : 0.042 0.140 1508 Planarity : 0.006 0.060 1676 Dihedral : 17.636 86.454 1840 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.10 % Allowed : 15.40 % Favored : 82.50 % 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: 0.65 (0.25), residues: 1160 helix: 1.42 (0.22), residues: 584 sheet: -0.04 (0.32), residues: 172 loop : -0.75 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS C 2 PHE 0.022 0.003 PHE G 124 TYR 0.014 0.003 TYR E 128 ARG 0.011 0.001 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.959 Fit side-chains REVERT: A 17 ARG cc_start: 0.7412 (ttm170) cc_final: 0.6779 (tmt170) REVERT: C 25 ILE cc_start: 0.8773 (mt) cc_final: 0.8274 (mt) REVERT: C 42 GLU cc_start: 0.8007 (tt0) cc_final: 0.7480 (pt0) REVERT: C 115 GLU cc_start: 0.7952 (mp0) cc_final: 0.7657 (mp0) REVERT: E 1 MET cc_start: 0.7877 (ptp) cc_final: 0.7519 (ptp) REVERT: G 1 MET cc_start: 0.7829 (ptp) cc_final: 0.7242 (ptp) REVERT: G 43 THR cc_start: 0.8333 (m) cc_final: 0.8010 (p) REVERT: B 42 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8101 (tm-30) REVERT: D 26 ARG cc_start: 0.7655 (mmm160) cc_final: 0.7423 (mmm160) REVERT: F 42 GLU cc_start: 0.8675 (tm-30) cc_final: 0.7605 (tm-30) REVERT: H 42 GLU cc_start: 0.8697 (tm-30) cc_final: 0.7433 (tm-30) outliers start: 21 outliers final: 16 residues processed: 186 average time/residue: 0.2395 time to fit residues: 59.9839 Evaluate side-chains 176 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain H residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 11 optimal weight: 0.0570 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 75 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.1104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 114 GLN E 114 GLN G 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.190900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.144173 restraints weight = 9503.031| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.04 r_work: 0.3393 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9784 Z= 0.223 Angle : 0.528 7.037 13336 Z= 0.278 Chirality : 0.039 0.135 1508 Planarity : 0.005 0.051 1676 Dihedral : 16.377 87.715 1840 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.90 % Allowed : 18.50 % Favored : 80.60 % 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: 0.83 (0.25), residues: 1160 helix: 1.48 (0.23), residues: 572 sheet: 0.11 (0.32), residues: 172 loop : -0.49 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 2 PHE 0.014 0.002 PHE G 124 TYR 0.011 0.002 TYR E 128 ARG 0.006 0.000 ARG F 7 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 178 time to evaluate : 1.021 Fit side-chains REVERT: A 17 ARG cc_start: 0.7406 (ttm170) cc_final: 0.6837 (tmt170) REVERT: A 37 ARG cc_start: 0.8125 (mpt180) cc_final: 0.7815 (mpt-90) REVERT: C 1 MET cc_start: 0.7537 (ptp) cc_final: 0.7280 (ptp) REVERT: C 42 GLU cc_start: 0.7919 (tt0) cc_final: 0.7559 (pt0) REVERT: C 115 GLU cc_start: 0.7950 (mp0) cc_final: 0.7696 (mp0) REVERT: E 1 MET cc_start: 0.7779 (ptp) cc_final: 0.7229 (ptp) REVERT: E 42 GLU cc_start: 0.7912 (tt0) cc_final: 0.7616 (tt0) REVERT: G 1 MET cc_start: 0.7806 (ptp) cc_final: 0.7302 (ptp) REVERT: G 43 THR cc_start: 0.8346 (m) cc_final: 0.8078 (p) REVERT: B 42 GLU cc_start: 0.8531 (tm-30) cc_final: 0.7555 (tm-30) REVERT: F 26 ARG cc_start: 0.7568 (mmm-85) cc_final: 0.6990 (mmm160) REVERT: F 42 GLU cc_start: 0.8549 (tm-30) cc_final: 0.7624 (tm-30) REVERT: H 26 ARG cc_start: 0.7485 (mmm160) cc_final: 0.7154 (mmm160) REVERT: H 42 GLU cc_start: 0.8563 (tm-30) cc_final: 0.7416 (tm-30) outliers start: 9 outliers final: 8 residues processed: 178 average time/residue: 0.2658 time to fit residues: 62.7329 Evaluate side-chains 170 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 12 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 26 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 114 GLN C 114 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.182080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.132581 restraints weight = 9520.094| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.07 r_work: 0.3224 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.070 9784 Z= 0.712 Angle : 0.732 7.346 13336 Z= 0.374 Chirality : 0.047 0.185 1508 Planarity : 0.006 0.055 1676 Dihedral : 18.218 89.955 1840 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.80 % Allowed : 18.10 % Favored : 79.10 % 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 (0.25), residues: 1160 helix: 1.04 (0.22), residues: 584 sheet: -0.11 (0.31), residues: 172 loop : -0.79 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS G 2 PHE 0.025 0.003 PHE C 124 TYR 0.022 0.003 TYR G 128 ARG 0.009 0.001 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.985 Fit side-chains REVERT: A 17 ARG cc_start: 0.7418 (ttm170) cc_final: 0.6803 (tmt170) REVERT: C 1 MET cc_start: 0.8207 (ptp) cc_final: 0.7850 (ptp) REVERT: C 25 ILE cc_start: 0.8916 (mt) cc_final: 0.8556 (mm) REVERT: C 42 GLU cc_start: 0.8027 (tt0) cc_final: 0.7619 (pt0) REVERT: E 1 MET cc_start: 0.8307 (ptp) cc_final: 0.7765 (ptp) REVERT: E 25 ILE cc_start: 0.8957 (mt) cc_final: 0.8611 (mm) REVERT: E 42 GLU cc_start: 0.8028 (tt0) cc_final: 0.7789 (tt0) REVERT: G 1 MET cc_start: 0.8216 (ptp) cc_final: 0.7883 (ptp) REVERT: B 26 ARG cc_start: 0.7727 (mmm160) cc_final: 0.7442 (mmm160) REVERT: B 42 GLU cc_start: 0.8748 (tm-30) cc_final: 0.7711 (tm-30) REVERT: D 26 ARG cc_start: 0.7604 (mmm160) cc_final: 0.7148 (mmm160) REVERT: D 56 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8468 (mt-10) REVERT: F 26 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.6926 (mmm160) REVERT: F 42 GLU cc_start: 0.8716 (tm-30) cc_final: 0.7794 (tm-30) REVERT: H 26 ARG cc_start: 0.7608 (mmm160) cc_final: 0.7040 (mmm160) REVERT: H 42 GLU cc_start: 0.8777 (tm-30) cc_final: 0.7794 (tm-30) REVERT: H 56 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8463 (mt-10) outliers start: 28 outliers final: 20 residues processed: 188 average time/residue: 0.3362 time to fit residues: 83.8669 Evaluate side-chains 185 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN E 114 GLN G 114 GLN D 30 GLN ** F 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.188611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.141252 restraints weight = 9383.510| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.99 r_work: 0.3371 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 9784 Z= 0.305 Angle : 0.570 7.521 13336 Z= 0.295 Chirality : 0.040 0.177 1508 Planarity : 0.005 0.059 1676 Dihedral : 16.593 88.981 1840 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.70 % Allowed : 19.10 % Favored : 79.20 % 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: 0.55 (0.25), residues: 1160 helix: 1.20 (0.23), residues: 572 sheet: -0.07 (0.32), residues: 172 loop : -0.50 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS G 2 PHE 0.013 0.002 PHE C 124 TYR 0.020 0.002 TYR G 128 ARG 0.007 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 1.123 Fit side-chains REVERT: A 1 MET cc_start: 0.7923 (ptp) cc_final: 0.7544 (ptp) REVERT: A 17 ARG cc_start: 0.7416 (ttm170) cc_final: 0.6891 (tmt170) REVERT: C 1 MET cc_start: 0.8040 (ptp) cc_final: 0.7771 (ptp) REVERT: C 25 ILE cc_start: 0.8931 (mt) cc_final: 0.8591 (mm) REVERT: C 42 GLU cc_start: 0.7880 (tt0) cc_final: 0.7639 (pt0) REVERT: E 1 MET cc_start: 0.8132 (ptp) cc_final: 0.7741 (ptp) REVERT: E 25 ILE cc_start: 0.8993 (mt) cc_final: 0.8711 (mm) REVERT: E 42 GLU cc_start: 0.7836 (tt0) cc_final: 0.7601 (tt0) REVERT: G 1 MET cc_start: 0.7985 (ptp) cc_final: 0.7769 (ptp) REVERT: B 42 GLU cc_start: 0.8561 (tm-30) cc_final: 0.7669 (tm-30) REVERT: D 26 ARG cc_start: 0.7694 (mmm160) cc_final: 0.7203 (mmm160) REVERT: F 26 ARG cc_start: 0.7601 (mmm-85) cc_final: 0.6973 (mmm160) REVERT: F 42 GLU cc_start: 0.8593 (tm-30) cc_final: 0.7820 (tm-30) REVERT: H 26 ARG cc_start: 0.7707 (mmm160) cc_final: 0.7380 (mmm160) REVERT: H 42 GLU cc_start: 0.8596 (tm-30) cc_final: 0.7899 (tm-30) outliers start: 17 outliers final: 15 residues processed: 173 average time/residue: 0.3489 time to fit residues: 80.0031 Evaluate side-chains 170 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 62 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 114 GLN G 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.190504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144387 restraints weight = 9483.688| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.95 r_work: 0.3398 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 9784 Z= 0.210 Angle : 0.536 6.601 13336 Z= 0.279 Chirality : 0.039 0.155 1508 Planarity : 0.005 0.054 1676 Dihedral : 15.165 78.579 1840 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.00 % Allowed : 20.00 % Favored : 79.00 % 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: 0.73 (0.25), residues: 1160 helix: 1.32 (0.22), residues: 572 sheet: 0.04 (0.33), residues: 172 loop : -0.37 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 2 PHE 0.018 0.002 PHE B 38 TYR 0.022 0.002 TYR E 121 ARG 0.007 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 1.098 Fit side-chains REVERT: A 17 ARG cc_start: 0.7349 (ttm170) cc_final: 0.6890 (tmt170) REVERT: A 47 MET cc_start: 0.8298 (mmm) cc_final: 0.8078 (mtp) REVERT: C 1 MET cc_start: 0.7746 (ptp) cc_final: 0.7462 (ptp) REVERT: C 17 ARG cc_start: 0.7182 (ttm110) cc_final: 0.6850 (tmm160) REVERT: C 25 ILE cc_start: 0.8935 (mt) cc_final: 0.8584 (mm) REVERT: C 42 GLU cc_start: 0.7910 (tt0) cc_final: 0.7696 (pt0) REVERT: E 1 MET cc_start: 0.7920 (ptp) cc_final: 0.7600 (ptp) REVERT: E 17 ARG cc_start: 0.7295 (ttm110) cc_final: 0.6870 (tmm160) REVERT: E 25 ILE cc_start: 0.8982 (mt) cc_final: 0.8697 (mm) REVERT: E 42 GLU cc_start: 0.7830 (tt0) cc_final: 0.7597 (tt0) REVERT: G 1 MET cc_start: 0.7722 (ptp) cc_final: 0.7477 (ptp) REVERT: G 43 THR cc_start: 0.8201 (m) cc_final: 0.7918 (p) REVERT: B 42 GLU cc_start: 0.8465 (tm-30) cc_final: 0.7633 (tm-30) REVERT: D 26 ARG cc_start: 0.7699 (mmm160) cc_final: 0.7192 (mmm160) REVERT: F 26 ARG cc_start: 0.7582 (mmm-85) cc_final: 0.7000 (mmm160) REVERT: F 42 GLU cc_start: 0.8473 (tm-30) cc_final: 0.7582 (tm-30) REVERT: H 26 ARG cc_start: 0.7705 (mmm160) cc_final: 0.7340 (mmm160) REVERT: H 42 GLU cc_start: 0.8522 (tm-30) cc_final: 0.7906 (tm-30) outliers start: 10 outliers final: 8 residues processed: 171 average time/residue: 0.2499 time to fit residues: 57.3473 Evaluate side-chains 167 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 62 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 9 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 95 optimal weight: 0.0570 chunk 28 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 114 GLN E 114 GLN G 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.191061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.144976 restraints weight = 9491.370| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.94 r_work: 0.3349 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 9784 Z= 0.307 Angle : 0.566 6.733 13336 Z= 0.291 Chirality : 0.040 0.149 1508 Planarity : 0.005 0.053 1676 Dihedral : 14.995 80.465 1840 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.30 % Allowed : 20.10 % Favored : 78.60 % 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: 0.71 (0.25), residues: 1160 helix: 1.33 (0.22), residues: 580 sheet: 0.02 (0.32), residues: 172 loop : -0.47 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS G 2 PHE 0.012 0.002 PHE C 124 TYR 0.019 0.003 TYR E 121 ARG 0.008 0.000 ARG F 7 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 1.018 Fit side-chains REVERT: A 1 MET cc_start: 0.7852 (ptp) cc_final: 0.7555 (ptp) REVERT: A 17 ARG cc_start: 0.7348 (ttm170) cc_final: 0.6914 (tmt170) REVERT: C 1 MET cc_start: 0.7872 (ptp) cc_final: 0.7664 (ptp) REVERT: C 17 ARG cc_start: 0.7213 (ttm110) cc_final: 0.6855 (tmm160) REVERT: C 25 ILE cc_start: 0.8957 (mt) cc_final: 0.8587 (mm) REVERT: C 42 GLU cc_start: 0.7920 (tt0) cc_final: 0.7665 (pt0) REVERT: E 1 MET cc_start: 0.8068 (ptp) cc_final: 0.7692 (ptp) REVERT: E 17 ARG cc_start: 0.7295 (ttm110) cc_final: 0.6889 (tmm160) REVERT: E 25 ILE cc_start: 0.9007 (mt) cc_final: 0.8688 (mm) REVERT: E 42 GLU cc_start: 0.7843 (tt0) cc_final: 0.7608 (tt0) REVERT: G 1 MET cc_start: 0.7843 (ptp) cc_final: 0.7566 (ptp) REVERT: G 17 ARG cc_start: 0.7423 (ttm110) cc_final: 0.7139 (tmt170) REVERT: G 42 GLU cc_start: 0.7881 (tt0) cc_final: 0.7606 (pt0) REVERT: G 43 THR cc_start: 0.8240 (m) cc_final: 0.7952 (p) REVERT: B 42 GLU cc_start: 0.8519 (tm-30) cc_final: 0.7736 (tm-30) REVERT: D 26 ARG cc_start: 0.7752 (mmm160) cc_final: 0.7190 (mmm160) REVERT: F 26 ARG cc_start: 0.7620 (mmm-85) cc_final: 0.7026 (mmm160) REVERT: F 42 GLU cc_start: 0.8519 (tm-30) cc_final: 0.7668 (tm-30) REVERT: H 26 ARG cc_start: 0.7762 (mmm160) cc_final: 0.7358 (mmm160) REVERT: H 42 GLU cc_start: 0.8570 (tm-30) cc_final: 0.7998 (tm-30) outliers start: 13 outliers final: 12 residues processed: 162 average time/residue: 0.3170 time to fit residues: 68.5560 Evaluate side-chains 166 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.190015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.143544 restraints weight = 9398.241| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.96 r_work: 0.3360 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9784 Z= 0.258 Angle : 0.549 6.864 13336 Z= 0.284 Chirality : 0.039 0.158 1508 Planarity : 0.004 0.052 1676 Dihedral : 14.554 87.861 1840 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.30 % Allowed : 20.20 % Favored : 78.50 % 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: 0.81 (0.25), residues: 1160 helix: 1.35 (0.22), residues: 572 sheet: 0.08 (0.32), residues: 172 loop : -0.27 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 2 PHE 0.009 0.002 PHE C 124 TYR 0.019 0.002 TYR E 121 ARG 0.008 0.000 ARG F 7 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 1.015 Fit side-chains REVERT: A 1 MET cc_start: 0.7791 (ptp) cc_final: 0.7473 (ptp) REVERT: A 17 ARG cc_start: 0.7311 (ttm170) cc_final: 0.6899 (tmt170) REVERT: C 1 MET cc_start: 0.7795 (ptp) cc_final: 0.7577 (ptp) REVERT: C 17 ARG cc_start: 0.7213 (ttm110) cc_final: 0.6878 (tmm160) REVERT: C 25 ILE cc_start: 0.8960 (mt) cc_final: 0.8567 (mm) REVERT: C 42 GLU cc_start: 0.7939 (tt0) cc_final: 0.7707 (pt0) REVERT: C 43 THR cc_start: 0.8250 (m) cc_final: 0.7877 (p) REVERT: E 1 MET cc_start: 0.7995 (ptp) cc_final: 0.7597 (ptp) REVERT: E 17 ARG cc_start: 0.7292 (ttm110) cc_final: 0.6891 (tmm160) REVERT: E 25 ILE cc_start: 0.9000 (mt) cc_final: 0.8668 (mm) REVERT: E 42 GLU cc_start: 0.7876 (tt0) cc_final: 0.7628 (tt0) REVERT: G 1 MET cc_start: 0.7791 (ptp) cc_final: 0.7542 (ptp) REVERT: G 17 ARG cc_start: 0.7410 (ttm110) cc_final: 0.7144 (tmt170) REVERT: G 43 THR cc_start: 0.8184 (m) cc_final: 0.7947 (p) REVERT: B 42 GLU cc_start: 0.8524 (tm-30) cc_final: 0.7662 (tm-30) REVERT: D 26 ARG cc_start: 0.7737 (mmm160) cc_final: 0.7136 (mmm160) REVERT: F 26 ARG cc_start: 0.7594 (mmm-85) cc_final: 0.7013 (mmm160) REVERT: F 42 GLU cc_start: 0.8522 (tm-30) cc_final: 0.7723 (tm-30) REVERT: H 26 ARG cc_start: 0.7720 (mmm160) cc_final: 0.7326 (mmm160) REVERT: H 42 GLU cc_start: 0.8552 (tm-30) cc_final: 0.7944 (tm-30) outliers start: 13 outliers final: 13 residues processed: 166 average time/residue: 0.2434 time to fit residues: 54.2522 Evaluate side-chains 169 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN G 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.186528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.139143 restraints weight = 9440.927| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.96 r_work: 0.3306 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 9784 Z= 0.366 Angle : 0.594 7.218 13336 Z= 0.305 Chirality : 0.041 0.165 1508 Planarity : 0.005 0.052 1676 Dihedral : 14.499 88.783 1840 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.50 % Allowed : 20.20 % Favored : 78.30 % 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: 0.61 (0.25), residues: 1160 helix: 1.23 (0.22), residues: 584 sheet: 0.02 (0.31), residues: 172 loop : -0.52 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS G 2 PHE 0.013 0.002 PHE C 124 TYR 0.019 0.003 TYR C 121 ARG 0.011 0.001 ARG D 7 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7927 (ptp) cc_final: 0.7573 (ptp) REVERT: A 17 ARG cc_start: 0.7307 (ttm170) cc_final: 0.6845 (tmt170) REVERT: C 1 MET cc_start: 0.7908 (ptp) cc_final: 0.7676 (ptp) REVERT: C 17 ARG cc_start: 0.7249 (ttm110) cc_final: 0.6836 (tmm160) REVERT: C 25 ILE cc_start: 0.8964 (mt) cc_final: 0.8585 (mm) REVERT: C 42 GLU cc_start: 0.8000 (tt0) cc_final: 0.7647 (pt0) REVERT: E 1 MET cc_start: 0.8131 (ptp) cc_final: 0.7711 (ptp) REVERT: E 17 ARG cc_start: 0.7295 (ttm110) cc_final: 0.6845 (tmm160) REVERT: E 25 ILE cc_start: 0.8981 (mt) cc_final: 0.8636 (mm) REVERT: E 42 GLU cc_start: 0.7845 (tt0) cc_final: 0.7598 (tt0) REVERT: G 1 MET cc_start: 0.7874 (ptp) cc_final: 0.7611 (ptp) REVERT: G 17 ARG cc_start: 0.7422 (ttm110) cc_final: 0.7066 (tmt170) REVERT: G 42 GLU cc_start: 0.7901 (tt0) cc_final: 0.7605 (pt0) REVERT: G 43 THR cc_start: 0.8234 (m) cc_final: 0.7938 (p) REVERT: B 42 GLU cc_start: 0.8581 (tm-30) cc_final: 0.7698 (tm-30) REVERT: F 26 ARG cc_start: 0.7590 (mmm-85) cc_final: 0.6990 (mmm160) REVERT: F 42 GLU cc_start: 0.8552 (tm-30) cc_final: 0.7702 (tm-30) REVERT: H 26 ARG cc_start: 0.7732 (mmm160) cc_final: 0.7321 (mmm160) REVERT: H 42 GLU cc_start: 0.8635 (tm-30) cc_final: 0.7970 (tm-30) outliers start: 15 outliers final: 15 residues processed: 163 average time/residue: 0.2466 time to fit residues: 54.4126 Evaluate side-chains 165 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 26 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 101 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN E 114 GLN G 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.191082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.144982 restraints weight = 9497.705| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.98 r_work: 0.3389 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9784 Z= 0.193 Angle : 0.534 7.545 13336 Z= 0.277 Chirality : 0.039 0.166 1508 Planarity : 0.004 0.053 1676 Dihedral : 13.562 87.918 1840 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.90 % Allowed : 20.90 % Favored : 78.20 % 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: 0.92 (0.25), residues: 1160 helix: 1.39 (0.22), residues: 572 sheet: 0.23 (0.33), residues: 172 loop : -0.20 (0.34), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 2 PHE 0.007 0.001 PHE G 137 TYR 0.019 0.002 TYR E 121 ARG 0.009 0.000 ARG B 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5572.82 seconds wall clock time: 98 minutes 19.93 seconds (5899.93 seconds total)