Starting phenix.real_space_refine on Wed Mar 4 00:33:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p3q_13182/03_2026/7p3q_13182_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p3q_13182/03_2026/7p3q_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 { model { file = "/net/cci-nas-00/data/ceres_data/7p3q_13182/03_2026/7p3q_13182_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p3q_13182/03_2026/7p3q_13182_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p3q_13182/03_2026/7p3q_13182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p3q_13182/03_2026/7p3q_13182.map" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.083 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: C, E, G, D, F, H Time building chain proxies: 1.63, per 1000 atoms: 0.17 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: 0.65 Conformation dependent library (CDL) restraints added in 352.8 milliseconds 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: 0.28 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: 1.36 Time building geometry restraints manager: 0.88 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 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' 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=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: 1.940 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.450 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.440 ------------------------------------------------------------------------------- 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 9816 Z= 0.623 Angle : 1.369 8.814 13386 Z= 0.967 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.001 ARG C 68 TYR 0.015 0.004 TYR E 121 PHE 0.027 0.004 PHE G 124 HIS 0.006 0.001 HIS E 2 Details of bonding type rmsd covalent geometry : bond 0.00873 ( 9784) covalent geometry : angle 1.34221 (13336) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.13778 ( 506) hydrogen bonds : angle 6.57447 ( 1518) metal coordination : bond 0.00608 ( 32) metal coordination : angle 4.69728 ( 48) *********************** 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 : 0.410 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: 0.7373 (p) outliers start: 4 outliers final: 0 residues processed: 207 average time/residue: 0.1223 time to fit residues: 33.3485 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 : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4210 r_free = 0.4210 target = 0.201793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.157600 restraints weight = 9531.559| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.01 r_work: 0.3511 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9816 Z= 0.149 Angle : 0.645 10.305 13386 Z= 0.308 Chirality : 0.039 0.126 1508 Planarity : 0.006 0.064 1676 Dihedral : 18.933 89.099 1840 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.70 % Allowed : 13.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.26), residues: 1160 helix: 2.14 (0.22), residues: 556 sheet: -0.13 (0.34), residues: 188 loop : -0.71 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 87 TYR 0.010 0.002 TYR E 121 PHE 0.011 0.002 PHE H 38 HIS 0.013 0.002 HIS A 2 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9784) covalent geometry : angle 0.57649 (13336) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04185 ( 506) hydrogen bonds : angle 4.95170 ( 1518) metal coordination : bond 0.00714 ( 32) metal coordination : angle 4.85169 ( 48) *********************** 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 187 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 180 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7458 (ttm170) cc_final: 0.6730 (tmt170) REVERT: A 43 THR cc_start: 0.8237 (m) cc_final: 0.7828 (p) REVERT: C 42 GLU cc_start: 0.7788 (tt0) cc_final: 0.7486 (pt0) REVERT: C 115 GLU cc_start: 0.7885 (mp0) cc_final: 0.7558 (mp0) REVERT: G 43 THR cc_start: 0.7804 (m) cc_final: 0.7536 (p) REVERT: F 26 ARG cc_start: 0.7382 (mmm160) cc_final: 0.7161 (mmm160) REVERT: H 26 ARG cc_start: 0.7514 (mmm160) cc_final: 0.7147 (mmm160) outliers start: 7 outliers final: 6 residues processed: 180 average time/residue: 0.1202 time to fit residues: 28.7065 Evaluate side-chains 167 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 161 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 30 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 = 0.4156 r_free = 0.4156 target = 0.197055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.151476 restraints weight = 9641.866| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.02 r_work: 0.3480 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9816 Z= 0.147 Angle : 0.596 9.369 13386 Z= 0.284 Chirality : 0.039 0.136 1508 Planarity : 0.005 0.054 1676 Dihedral : 16.909 89.145 1840 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.90 % Allowed : 15.40 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.26), residues: 1160 helix: 1.88 (0.23), residues: 564 sheet: 0.44 (0.33), residues: 168 loop : -0.69 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 87 TYR 0.012 0.002 TYR E 128 PHE 0.012 0.002 PHE G 124 HIS 0.006 0.001 HIS G 2 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9784) covalent geometry : angle 0.52910 (13336) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03966 ( 506) hydrogen bonds : angle 4.56441 ( 1518) metal coordination : bond 0.00756 ( 32) metal coordination : angle 4.62560 ( 48) *********************** 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 179 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 170 time to evaluate : 0.344 Fit side-chains REVERT: A 17 ARG cc_start: 0.7422 (ttm170) cc_final: 0.6884 (tmt170) REVERT: A 43 THR cc_start: 0.8372 (m) cc_final: 0.7929 (p) REVERT: C 42 GLU cc_start: 0.7847 (tt0) cc_final: 0.7446 (pt0) REVERT: C 115 GLU cc_start: 0.7813 (mp0) cc_final: 0.7570 (mp0) REVERT: E 1 MET cc_start: 0.7498 (ptp) cc_final: 0.7131 (ptp) REVERT: G 1 MET cc_start: 0.7725 (ptp) cc_final: 0.7066 (ptp) REVERT: G 43 THR cc_start: 0.7999 (m) cc_final: 0.7740 (p) REVERT: B 42 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7889 (tm-30) REVERT: D 26 ARG cc_start: 0.7656 (mmm160) cc_final: 0.7264 (mmm160) REVERT: F 42 GLU cc_start: 0.8485 (tm-30) cc_final: 0.7515 (tm-30) REVERT: H 42 GLU cc_start: 0.8539 (tm-30) cc_final: 0.7462 (tm-30) outliers start: 9 outliers final: 4 residues processed: 175 average time/residue: 0.1094 time to fit residues: 25.8283 Evaluate side-chains 159 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 155 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** 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 = 0.4086 r_free = 0.4086 target = 0.189863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.142980 restraints weight = 9609.176| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.02 r_work: 0.3328 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 9816 Z= 0.259 Angle : 0.692 10.594 13386 Z= 0.323 Chirality : 0.042 0.131 1508 Planarity : 0.006 0.051 1676 Dihedral : 16.732 86.919 1840 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.40 % Allowed : 16.80 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.25), residues: 1160 helix: 1.50 (0.23), residues: 576 sheet: -0.02 (0.32), residues: 172 loop : -0.62 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 7 TYR 0.009 0.002 TYR D 128 PHE 0.022 0.003 PHE C 124 HIS 0.006 0.002 HIS G 2 Details of bonding type rmsd covalent geometry : bond 0.00611 ( 9784) covalent geometry : angle 0.61456 (13336) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04406 ( 506) hydrogen bonds : angle 4.92422 ( 1518) metal coordination : bond 0.01129 ( 32) metal coordination : angle 5.34757 ( 48) *********************** 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 189 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.296 Fit side-chains REVERT: A 1 MET cc_start: 0.7414 (ptp) cc_final: 0.6572 (ptp) REVERT: A 17 ARG cc_start: 0.7372 (ttm170) cc_final: 0.6819 (tmt170) REVERT: A 37 ARG cc_start: 0.8013 (mpt180) cc_final: 0.7729 (mpt-90) REVERT: C 1 MET cc_start: 0.7949 (ptp) cc_final: 0.7543 (ptp) REVERT: C 42 GLU cc_start: 0.7989 (tt0) cc_final: 0.7552 (pt0) REVERT: C 115 GLU cc_start: 0.7957 (mp0) cc_final: 0.7689 (mp0) REVERT: E 1 MET cc_start: 0.8149 (ptp) cc_final: 0.7643 (ptp) REVERT: G 1 MET cc_start: 0.8088 (ptp) cc_final: 0.7629 (ptp) REVERT: G 37 ARG cc_start: 0.7989 (mpt180) cc_final: 0.7766 (mpt-90) REVERT: G 43 THR cc_start: 0.8452 (m) cc_final: 0.8159 (p) REVERT: B 42 GLU cc_start: 0.8619 (tm-30) cc_final: 0.7562 (tm-30) REVERT: D 26 ARG cc_start: 0.7645 (mmm160) cc_final: 0.7428 (mmm160) REVERT: D 42 GLU cc_start: 0.8774 (tm-30) cc_final: 0.7166 (tm-30) REVERT: F 26 ARG cc_start: 0.7571 (mmm160) cc_final: 0.7086 (mmm160) REVERT: F 42 GLU cc_start: 0.8594 (tm-30) cc_final: 0.7646 (tm-30) REVERT: H 26 ARG cc_start: 0.7658 (mmm160) cc_final: 0.7284 (mmm160) REVERT: H 42 GLU cc_start: 0.8675 (tm-30) cc_final: 0.7630 (tm-30) outliers start: 14 outliers final: 14 residues processed: 182 average time/residue: 0.1157 time to fit residues: 28.2247 Evaluate side-chains 172 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.188035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.141220 restraints weight = 9577.621| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.99 r_work: 0.3337 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 9816 Z= 0.232 Angle : 0.650 9.861 13386 Z= 0.301 Chirality : 0.040 0.133 1508 Planarity : 0.005 0.055 1676 Dihedral : 16.295 89.693 1840 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.60 % Allowed : 18.50 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.25), residues: 1160 helix: 1.43 (0.23), residues: 568 sheet: 0.00 (0.32), residues: 172 loop : -0.42 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 7 TYR 0.016 0.002 TYR E 121 PHE 0.016 0.002 PHE G 124 HIS 0.009 0.002 HIS A 2 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 9784) covalent geometry : angle 0.56915 (13336) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04240 ( 506) hydrogen bonds : angle 4.82302 ( 1518) metal coordination : bond 0.01045 ( 32) metal coordination : angle 5.27835 ( 48) *********************** 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 187 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7376 (ttm170) cc_final: 0.6825 (tmt170) REVERT: A 37 ARG cc_start: 0.8032 (mpt180) cc_final: 0.7826 (mpt-90) REVERT: C 1 MET cc_start: 0.7998 (ptp) cc_final: 0.7542 (ptp) REVERT: C 25 ILE cc_start: 0.8846 (mt) cc_final: 0.8439 (mm) REVERT: C 42 GLU cc_start: 0.7948 (tt0) cc_final: 0.7643 (pt0) REVERT: C 115 GLU cc_start: 0.7924 (mp0) cc_final: 0.7645 (mp0) REVERT: E 1 MET cc_start: 0.8101 (ptp) cc_final: 0.7612 (ptp) REVERT: G 1 MET cc_start: 0.8061 (ptp) cc_final: 0.7766 (ptp) REVERT: G 37 ARG cc_start: 0.8065 (mpt180) cc_final: 0.7864 (mpt-90) REVERT: G 43 THR cc_start: 0.8516 (m) cc_final: 0.8238 (p) REVERT: B 42 GLU cc_start: 0.8541 (tm-30) cc_final: 0.7500 (tm-30) REVERT: D 26 ARG cc_start: 0.7612 (mmm160) cc_final: 0.7390 (mmm160) REVERT: F 26 ARG cc_start: 0.7588 (mmm160) cc_final: 0.7185 (mmm160) REVERT: F 42 GLU cc_start: 0.8562 (tm-30) cc_final: 0.7728 (tm-30) REVERT: H 26 ARG cc_start: 0.7731 (mmm160) cc_final: 0.7451 (mmm160) REVERT: H 42 GLU cc_start: 0.8615 (tm-30) cc_final: 0.7772 (tm-30) outliers start: 16 outliers final: 10 residues processed: 179 average time/residue: 0.1180 time to fit residues: 27.9612 Evaluate side-chains 173 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain D residue 100 LEU 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 105 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.188248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.140807 restraints weight = 9498.744| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.05 r_work: 0.3330 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 9816 Z= 0.212 Angle : 0.646 10.316 13386 Z= 0.298 Chirality : 0.040 0.141 1508 Planarity : 0.005 0.054 1676 Dihedral : 15.776 89.394 1840 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.20 % Allowed : 18.90 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.25), residues: 1160 helix: 1.41 (0.23), residues: 568 sheet: 0.02 (0.32), residues: 172 loop : -0.39 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 87 TYR 0.015 0.002 TYR E 121 PHE 0.014 0.002 PHE G 124 HIS 0.008 0.001 HIS A 2 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 9784) covalent geometry : angle 0.56504 (13336) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04186 ( 506) hydrogen bonds : angle 4.78962 ( 1518) metal coordination : bond 0.00997 ( 32) metal coordination : angle 5.24935 ( 48) *********************** 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 176 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.287 Fit side-chains REVERT: A 17 ARG cc_start: 0.7355 (ttm170) cc_final: 0.6865 (tmt170) REVERT: C 1 MET cc_start: 0.7987 (ptp) cc_final: 0.7702 (ptp) REVERT: C 17 ARG cc_start: 0.7150 (ttm110) cc_final: 0.6720 (tmm160) REVERT: C 25 ILE cc_start: 0.8884 (mt) cc_final: 0.8490 (mm) REVERT: C 42 GLU cc_start: 0.7954 (tt0) cc_final: 0.7652 (pt0) REVERT: C 115 GLU cc_start: 0.7891 (mp0) cc_final: 0.7611 (mp0) REVERT: E 1 MET cc_start: 0.8124 (ptp) cc_final: 0.7671 (ptp) REVERT: G 1 MET cc_start: 0.8058 (ptp) cc_final: 0.7749 (ptp) REVERT: G 43 THR cc_start: 0.8533 (m) cc_final: 0.8293 (p) REVERT: B 26 ARG cc_start: 0.7712 (mmm160) cc_final: 0.7462 (mmm160) REVERT: B 42 GLU cc_start: 0.8520 (tm-30) cc_final: 0.7673 (tm-30) REVERT: D 26 ARG cc_start: 0.7616 (mmm160) cc_final: 0.7386 (mmm160) REVERT: D 42 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8073 (tm-30) REVERT: F 26 ARG cc_start: 0.7608 (mmm160) cc_final: 0.7326 (mmm160) REVERT: F 42 GLU cc_start: 0.8576 (tm-30) cc_final: 0.7708 (tm-30) REVERT: H 26 ARG cc_start: 0.7772 (mmm160) cc_final: 0.7414 (mmm160) REVERT: H 42 GLU cc_start: 0.8596 (tm-30) cc_final: 0.7869 (tm-30) outliers start: 12 outliers final: 11 residues processed: 172 average time/residue: 0.1203 time to fit residues: 27.3180 Evaluate side-chains 172 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 44 CYS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain E residue 44 CYS 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 61 THR Chi-restraints excluded: chain F residue 77 THR 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 53 optimal weight: 0.0170 chunk 51 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 chunk 86 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 chunk 59 optimal weight: 0.0770 chunk 69 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 = 0.4129 r_free = 0.4129 target = 0.194902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.150086 restraints weight = 9541.867| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.96 r_work: 0.3445 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 9816 Z= 0.111 Angle : 0.580 9.948 13386 Z= 0.270 Chirality : 0.038 0.161 1508 Planarity : 0.004 0.053 1676 Dihedral : 14.359 75.514 1840 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.70 % Allowed : 19.70 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.25), residues: 1160 helix: 1.56 (0.23), residues: 568 sheet: 0.01 (0.31), residues: 192 loop : -0.31 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 87 TYR 0.019 0.002 TYR E 121 PHE 0.007 0.001 PHE B 38 HIS 0.011 0.001 HIS A 2 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 9784) covalent geometry : angle 0.50111 (13336) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03718 ( 506) hydrogen bonds : angle 4.44497 ( 1518) metal coordination : bond 0.00715 ( 32) metal coordination : angle 4.90332 ( 48) *********************** 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 158 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7215 (ttm170) cc_final: 0.6884 (tmt170) REVERT: C 1 MET cc_start: 0.7613 (ptp) cc_final: 0.7302 (ptp) REVERT: C 17 ARG cc_start: 0.7126 (ttm110) cc_final: 0.6871 (tmt170) REVERT: C 25 ILE cc_start: 0.8897 (mt) cc_final: 0.8511 (mm) REVERT: C 43 THR cc_start: 0.8107 (m) cc_final: 0.7712 (p) REVERT: E 1 MET cc_start: 0.7820 (ptp) cc_final: 0.7470 (ptp) REVERT: E 17 ARG cc_start: 0.7396 (ttm110) cc_final: 0.6940 (tmm160) REVERT: E 25 ILE cc_start: 0.8954 (mt) cc_final: 0.8615 (mm) REVERT: G 1 MET cc_start: 0.7746 (ptp) cc_final: 0.7524 (ptp) REVERT: G 17 ARG cc_start: 0.7429 (ttm110) cc_final: 0.7138 (tmt170) REVERT: B 42 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7592 (tm-30) REVERT: D 42 GLU cc_start: 0.8477 (tm-30) cc_final: 0.7746 (tm-30) REVERT: F 26 ARG cc_start: 0.7637 (mmm160) cc_final: 0.7229 (mmm160) REVERT: F 42 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7639 (tm-30) REVERT: H 26 ARG cc_start: 0.7829 (mmm160) cc_final: 0.7435 (mmm160) REVERT: H 42 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7874 (tm-30) outliers start: 7 outliers final: 5 residues processed: 155 average time/residue: 0.1173 time to fit residues: 24.2934 Evaluate side-chains 150 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 145 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 100 LEU Chi-restraints excluded: chain D residue 100 LEU 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 104 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.190928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.144690 restraints weight = 9415.300| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.97 r_work: 0.3382 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9816 Z= 0.185 Angle : 0.621 9.507 13386 Z= 0.288 Chirality : 0.040 0.176 1508 Planarity : 0.005 0.051 1676 Dihedral : 14.350 80.587 1840 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.90 % Allowed : 19.80 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.25), residues: 1160 helix: 1.55 (0.22), residues: 576 sheet: 0.03 (0.31), residues: 192 loop : -0.39 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 87 TYR 0.017 0.002 TYR G 128 PHE 0.012 0.002 PHE G 124 HIS 0.010 0.001 HIS A 2 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 9784) covalent geometry : angle 0.54407 (13336) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03953 ( 506) hydrogen bonds : angle 4.54081 ( 1518) metal coordination : bond 0.00894 ( 32) metal coordination : angle 5.03841 ( 48) *********************** 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: 9 poor density : 158 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7291 (ttm170) cc_final: 0.6924 (tmt170) REVERT: C 1 MET cc_start: 0.7831 (ptp) cc_final: 0.7598 (ptp) REVERT: C 17 ARG cc_start: 0.7129 (ttm110) cc_final: 0.6793 (tmm160) REVERT: C 43 THR cc_start: 0.8191 (m) cc_final: 0.7865 (p) REVERT: E 1 MET cc_start: 0.7975 (ptp) cc_final: 0.7608 (ptp) REVERT: E 17 ARG cc_start: 0.7429 (ttm110) cc_final: 0.6977 (tmm160) REVERT: E 25 ILE cc_start: 0.8979 (mt) cc_final: 0.8626 (mm) REVERT: G 1 MET cc_start: 0.7877 (ptp) cc_final: 0.7673 (ptp) REVERT: G 17 ARG cc_start: 0.7448 (ttm110) cc_final: 0.7139 (tmt170) REVERT: G 25 ILE cc_start: 0.9108 (mt) cc_final: 0.8576 (mp) REVERT: G 42 GLU cc_start: 0.8119 (tt0) cc_final: 0.7800 (pt0) REVERT: B 42 GLU cc_start: 0.8411 (tm-30) cc_final: 0.7613 (tm-30) REVERT: D 42 GLU cc_start: 0.8501 (tm-30) cc_final: 0.7700 (tm-30) REVERT: F 26 ARG cc_start: 0.7657 (mmm160) cc_final: 0.7208 (mmm160) REVERT: F 42 GLU cc_start: 0.8498 (tm-30) cc_final: 0.7666 (tm-30) REVERT: H 26 ARG cc_start: 0.7808 (mmm160) cc_final: 0.7377 (mmm160) REVERT: H 42 GLU cc_start: 0.8515 (tm-30) cc_final: 0.7963 (tm-30) outliers start: 9 outliers final: 7 residues processed: 161 average time/residue: 0.1047 time to fit residues: 22.8323 Evaluate side-chains 161 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain C residue 44 CYS 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 D residue 101 THR Chi-restraints excluded: chain H residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 86 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4123 r_free = 0.4123 target = 0.194034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.148813 restraints weight = 9472.414| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.95 r_work: 0.3417 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9816 Z= 0.137 Angle : 0.603 9.963 13386 Z= 0.279 Chirality : 0.039 0.189 1508 Planarity : 0.004 0.052 1676 Dihedral : 13.918 86.470 1840 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.80 % Allowed : 20.40 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.25), residues: 1160 helix: 1.56 (0.22), residues: 580 sheet: 0.30 (0.32), residues: 172 loop : -0.44 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 7 TYR 0.019 0.002 TYR E 121 PHE 0.008 0.001 PHE C 124 HIS 0.010 0.001 HIS A 2 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9784) covalent geometry : angle 0.52371 (13336) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03775 ( 506) hydrogen bonds : angle 4.41832 ( 1518) metal coordination : bond 0.00763 ( 32) metal coordination : angle 5.02272 ( 48) *********************** 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 162 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7215 (ttm170) cc_final: 0.6909 (tmt170) REVERT: C 1 MET cc_start: 0.7690 (ptp) cc_final: 0.7304 (ptp) REVERT: C 43 THR cc_start: 0.8147 (m) cc_final: 0.7882 (p) REVERT: E 1 MET cc_start: 0.7860 (ptp) cc_final: 0.7455 (ptp) REVERT: E 17 ARG cc_start: 0.7432 (ttm110) cc_final: 0.7026 (tmm160) REVERT: E 25 ILE cc_start: 0.8979 (mt) cc_final: 0.8633 (mm) REVERT: G 1 MET cc_start: 0.7843 (ptp) cc_final: 0.7594 (ptp) REVERT: G 17 ARG cc_start: 0.7399 (ttm110) cc_final: 0.7175 (tmt170) REVERT: B 42 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7811 (tm-30) REVERT: D 42 GLU cc_start: 0.8453 (tt0) cc_final: 0.7595 (tm-30) REVERT: F 26 ARG cc_start: 0.7660 (mmm160) cc_final: 0.7227 (mmm160) REVERT: F 42 GLU cc_start: 0.8480 (tm-30) cc_final: 0.7608 (tm-30) REVERT: H 26 ARG cc_start: 0.7806 (mmm160) cc_final: 0.7404 (mmm160) REVERT: H 42 GLU cc_start: 0.8467 (tm-30) cc_final: 0.7933 (tm-30) outliers start: 8 outliers final: 7 residues processed: 158 average time/residue: 0.1114 time to fit residues: 23.9262 Evaluate side-chains 156 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 149 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain C residue 44 CYS 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 H residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.187540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.140664 restraints weight = 9386.639| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.94 r_work: 0.3320 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9816 Z= 0.265 Angle : 0.685 9.964 13386 Z= 0.319 Chirality : 0.041 0.158 1508 Planarity : 0.005 0.051 1676 Dihedral : 14.285 89.369 1840 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.70 % Allowed : 20.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.25), residues: 1160 helix: 1.38 (0.22), residues: 580 sheet: 0.06 (0.31), residues: 172 loop : -0.39 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 7 TYR 0.022 0.003 TYR A 128 PHE 0.015 0.002 PHE C 124 HIS 0.011 0.002 HIS A 2 Details of bonding type rmsd covalent geometry : bond 0.00619 ( 9784) covalent geometry : angle 0.61081 (13336) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04266 ( 506) hydrogen bonds : angle 4.73182 ( 1518) metal coordination : bond 0.01115 ( 32) metal coordination : angle 5.21014 ( 48) ********************** 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 159 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 152 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7270 (ttm170) cc_final: 0.6900 (tmt170) REVERT: C 1 MET cc_start: 0.7948 (ptp) cc_final: 0.7729 (ptp) REVERT: C 17 ARG cc_start: 0.8048 (tmt170) cc_final: 0.7462 (tmm160) REVERT: E 1 MET cc_start: 0.8153 (ptp) cc_final: 0.7714 (ptp) REVERT: E 17 ARG cc_start: 0.7454 (ttm110) cc_final: 0.6939 (tmm160) REVERT: E 25 ILE cc_start: 0.8974 (mt) cc_final: 0.8622 (mm) REVERT: G 1 MET cc_start: 0.8015 (ptp) cc_final: 0.7773 (ptp) REVERT: G 17 ARG cc_start: 0.7457 (ttm110) cc_final: 0.7104 (tmt170) REVERT: G 25 ILE cc_start: 0.9069 (mp) cc_final: 0.8660 (mm) REVERT: B 42 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7682 (tm-30) REVERT: D 42 GLU cc_start: 0.8577 (tt0) cc_final: 0.7651 (tm-30) REVERT: F 26 ARG cc_start: 0.7629 (mmm160) cc_final: 0.7168 (mmm160) REVERT: F 42 GLU cc_start: 0.8543 (tm-30) cc_final: 0.7668 (tm-30) REVERT: H 26 ARG cc_start: 0.7851 (mmm160) cc_final: 0.7415 (mmm160) REVERT: H 42 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8001 (tm-30) outliers start: 7 outliers final: 7 residues processed: 156 average time/residue: 0.1121 time to fit residues: 23.4782 Evaluate side-chains 159 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 152 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS 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 100 LEU Chi-restraints excluded: chain D residue 100 LEU 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 102 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 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 G 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.194860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.149561 restraints weight = 9418.685| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.95 r_work: 0.3412 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9816 Z= 0.136 Angle : 0.623 10.089 13386 Z= 0.287 Chirality : 0.039 0.169 1508 Planarity : 0.004 0.054 1676 Dihedral : 13.641 89.334 1840 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.60 % Allowed : 21.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.25), residues: 1160 helix: 1.41 (0.22), residues: 576 sheet: 0.19 (0.31), residues: 172 loop : -0.21 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 7 TYR 0.020 0.002 TYR E 121 PHE 0.008 0.001 PHE G 137 HIS 0.011 0.001 HIS A 2 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9784) covalent geometry : angle 0.54445 (13336) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03820 ( 506) hydrogen bonds : angle 4.44353 ( 1518) metal coordination : bond 0.00758 ( 32) metal coordination : angle 5.09494 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2604.83 seconds wall clock time: 45 minutes 14.50 seconds (2714.50 seconds total)