Starting phenix.real_space_refine on Sun Jul 27 17:54:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p3q_13182/07_2025/7p3q_13182_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p3q_13182/07_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_13182/07_2025/7p3q_13182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p3q_13182/07_2025/7p3q_13182.map" model { file = "/net/cci-nas-00/data/ceres_data/7p3q_13182/07_2025/7p3q_13182_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p3q_13182/07_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-5711/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: 4.52, per 1000 atoms: 0.47 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: 3.08 Conformation dependent library (CDL) restraints added in 1.3 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: 1.10 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: 2.95 Time building geometry restraints manager: 3.56 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 76.90 31.69 45.21 1 1.00e+01 1.00e-02 2.84e+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: 0.08 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: 2.440 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.010 Find NCS groups from input model: 0.210 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:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.650 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.13778 ( 506) hydrogen bonds : angle 6.57447 ( 1518) metal coordination : bond 0.00608 ( 32) metal coordination : angle 4.69728 ( 48) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00873 ( 9784) covalent geometry : angle 1.34221 (13336) *********************** 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 : 1.342 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: 0.2886 time to fit residues: 79.2872 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 : 1.002 ------------------------------------------------------------------------------- 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: 7.9990 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: 20.0000 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.4163 r_free = 0.4163 target = 0.197545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.151647 restraints weight = 9446.058| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.08 r_work: 0.3469 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 9816 Z= 0.166 Angle : 0.655 10.185 13386 Z= 0.312 Chirality : 0.039 0.129 1508 Planarity : 0.006 0.065 1676 Dihedral : 18.849 88.128 1840 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: 1.13 (0.25), residues: 1160 helix: 2.05 (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 0.011 0.002 HIS A 2 PHE 0.011 0.002 PHE H 38 TYR 0.011 0.002 TYR E 121 ARG 0.009 0.001 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 506) hydrogen bonds : angle 4.96487 ( 1518) metal coordination : bond 0.00765 ( 32) metal coordination : angle 4.93330 ( 48) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00368 ( 9784) covalent geometry : angle 0.58573 (13336) *********************** 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 185 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 1.297 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7465 (ttm170) cc_final: 0.6741 (tmt170) REVERT: A 43 THR cc_start: 0.8295 (m) cc_final: 0.7872 (p) REVERT: C 42 GLU cc_start: 0.7817 (tt0) cc_final: 0.7506 (pt0) REVERT: C 115 GLU cc_start: 0.7902 (mp0) cc_final: 0.7579 (mp0) REVERT: G 43 THR cc_start: 0.7876 (m) cc_final: 0.7623 (p) REVERT: D 26 ARG cc_start: 0.7539 (mmm160) cc_final: 0.7155 (mmm160) REVERT: F 26 ARG cc_start: 0.7385 (mmm160) cc_final: 0.7159 (mmm160) outliers start: 8 outliers final: 7 residues processed: 177 average time/residue: 0.2857 time to fit residues: 67.6086 Evaluate side-chains 170 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 163 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 43 THR 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 100 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.191871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.145272 restraints weight = 9583.152| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.01 r_work: 0.3392 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9816 Z= 0.220 Angle : 0.654 9.613 13386 Z= 0.309 Chirality : 0.040 0.139 1508 Planarity : 0.005 0.059 1676 Dihedral : 17.358 88.240 1840 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.30 % Allowed : 15.60 % Favored : 83.10 % 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: 0.77 (0.25), residues: 1160 helix: 1.55 (0.23), residues: 584 sheet: 0.08 (0.33), residues: 172 loop : -0.77 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS G 2 PHE 0.019 0.002 PHE G 124 TYR 0.013 0.002 TYR E 128 ARG 0.014 0.001 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.04315 ( 506) hydrogen bonds : angle 4.82414 ( 1518) metal coordination : bond 0.00987 ( 32) metal coordination : angle 4.98755 ( 48) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00514 ( 9784) covalent geometry : angle 0.58314 (13336) *********************** 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 191 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 1.093 Fit side-chains REVERT: A 17 ARG cc_start: 0.7406 (ttm170) cc_final: 0.6875 (tmt170) REVERT: C 1 MET cc_start: 0.7730 (ptp) cc_final: 0.7482 (ptp) REVERT: C 25 ILE cc_start: 0.8762 (mt) cc_final: 0.8310 (mt) REVERT: C 42 GLU cc_start: 0.7945 (tt0) cc_final: 0.7599 (pt0) REVERT: C 115 GLU cc_start: 0.7911 (mp0) cc_final: 0.7641 (mp0) REVERT: E 1 MET cc_start: 0.7822 (ptp) cc_final: 0.7476 (ptp) REVERT: G 1 MET cc_start: 0.7873 (ptp) cc_final: 0.7234 (ptp) REVERT: G 43 THR cc_start: 0.8244 (m) cc_final: 0.7932 (p) REVERT: B 42 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7238 (tm-30) REVERT: D 26 ARG cc_start: 0.7693 (mmm160) cc_final: 0.7454 (mmm160) REVERT: D 42 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8211 (tm-30) REVERT: F 42 GLU cc_start: 0.8588 (tm-30) cc_final: 0.7406 (tm-30) REVERT: H 42 GLU cc_start: 0.8618 (tm-30) cc_final: 0.7475 (tm-30) outliers start: 13 outliers final: 10 residues processed: 185 average time/residue: 0.2570 time to fit residues: 64.3536 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 : 1.165 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 91 optimal weight: 0.3980 chunk 43 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4072 r_free = 0.4072 target = 0.188935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.142165 restraints weight = 9478.944| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.98 r_work: 0.3390 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9816 Z= 0.225 Angle : 0.647 10.280 13386 Z= 0.301 Chirality : 0.040 0.126 1508 Planarity : 0.005 0.053 1676 Dihedral : 16.744 86.508 1840 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.40 % Allowed : 17.50 % Favored : 81.10 % 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: 0.76 (0.25), residues: 1160 helix: 1.53 (0.23), residues: 576 sheet: -0.00 (0.32), residues: 172 loop : -0.69 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 2 PHE 0.016 0.002 PHE C 124 TYR 0.019 0.002 TYR G 128 ARG 0.005 0.000 ARG H 26 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 506) hydrogen bonds : angle 4.80431 ( 1518) metal coordination : bond 0.00993 ( 32) metal coordination : angle 5.17403 ( 48) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00523 ( 9784) covalent geometry : angle 0.56867 (13336) *********************** 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 190 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 1.078 Fit side-chains REVERT: A 1 MET cc_start: 0.7481 (ptp) cc_final: 0.6792 (ptp) REVERT: A 17 ARG cc_start: 0.7396 (ttm170) cc_final: 0.6884 (tmt170) REVERT: A 37 ARG cc_start: 0.8072 (mpt180) cc_final: 0.7776 (mpt-90) REVERT: C 1 MET cc_start: 0.8015 (ptp) cc_final: 0.7709 (ptp) REVERT: C 42 GLU cc_start: 0.7911 (tt0) cc_final: 0.7587 (pt0) REVERT: C 115 GLU cc_start: 0.7948 (mp0) cc_final: 0.7681 (mp0) REVERT: E 1 MET cc_start: 0.8008 (ptp) cc_final: 0.7548 (ptp) REVERT: E 42 GLU cc_start: 0.7879 (tt0) cc_final: 0.7595 (tt0) REVERT: G 1 MET cc_start: 0.7976 (ptp) cc_final: 0.7607 (ptp) REVERT: G 37 ARG cc_start: 0.7939 (mpt180) cc_final: 0.7653 (mpt-90) REVERT: G 43 THR cc_start: 0.8449 (m) cc_final: 0.8155 (p) REVERT: B 42 GLU cc_start: 0.8524 (tm-30) cc_final: 0.7468 (tm-30) REVERT: D 26 ARG cc_start: 0.7690 (mmm160) cc_final: 0.7460 (mmm160) REVERT: D 42 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8375 (tm-30) REVERT: F 42 GLU cc_start: 0.8556 (tm-30) cc_final: 0.7625 (tm-30) REVERT: H 26 ARG cc_start: 0.7646 (mmm160) cc_final: 0.7290 (mmm160) REVERT: H 42 GLU cc_start: 0.8643 (tm-30) cc_final: 0.7656 (tm-30) outliers start: 14 outliers final: 14 residues processed: 181 average time/residue: 0.2741 time to fit residues: 66.4501 Evaluate side-chains 177 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 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 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 29 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 ** 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 = 0.4052 r_free = 0.4052 target = 0.186551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.138506 restraints weight = 9490.950| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.99 r_work: 0.3283 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 9816 Z= 0.328 Angle : 0.731 10.359 13386 Z= 0.340 Chirality : 0.043 0.130 1508 Planarity : 0.006 0.058 1676 Dihedral : 17.259 89.137 1840 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.40 % Allowed : 18.00 % 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 (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: 0.42 (0.25), residues: 1160 helix: 1.20 (0.22), residues: 584 sheet: -0.12 (0.32), residues: 172 loop : -0.83 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS E 2 PHE 0.022 0.003 PHE G 124 TYR 0.021 0.003 TYR G 128 ARG 0.005 0.001 ARG F 7 Details of bonding type rmsd hydrogen bonds : bond 0.04630 ( 506) hydrogen bonds : angle 5.12399 ( 1518) metal coordination : bond 0.01328 ( 32) metal coordination : angle 5.42470 ( 48) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00780 ( 9784) covalent geometry : angle 0.65557 (13336) *********************** 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 197 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 1.756 Fit side-chains REVERT: A 1 MET cc_start: 0.7859 (ptp) cc_final: 0.7092 (ptp) REVERT: A 17 ARG cc_start: 0.7422 (ttm170) cc_final: 0.6879 (tmt170) REVERT: C 1 MET cc_start: 0.8295 (ptp) cc_final: 0.7969 (ptp) REVERT: C 25 ILE cc_start: 0.8920 (mt) cc_final: 0.8548 (mm) REVERT: C 42 GLU cc_start: 0.7987 (tt0) cc_final: 0.7672 (pt0) REVERT: E 1 MET cc_start: 0.8276 (ptp) cc_final: 0.7913 (ptp) REVERT: E 25 ILE cc_start: 0.8946 (mt) cc_final: 0.8640 (mm) REVERT: E 42 GLU cc_start: 0.7872 (tt0) cc_final: 0.7615 (tt0) REVERT: G 1 MET cc_start: 0.8180 (ptp) cc_final: 0.7931 (ptp) REVERT: G 37 ARG cc_start: 0.8085 (mpt180) cc_final: 0.7835 (mpt-90) REVERT: G 43 THR cc_start: 0.8617 (m) cc_final: 0.8335 (p) REVERT: B 26 ARG cc_start: 0.7715 (mmm160) cc_final: 0.7468 (mmm160) REVERT: B 42 GLU cc_start: 0.8608 (tm-30) cc_final: 0.7529 (tm-30) REVERT: D 26 ARG cc_start: 0.7639 (mmm160) cc_final: 0.7383 (mmm160) REVERT: D 42 GLU cc_start: 0.8751 (tm-30) cc_final: 0.7880 (tm-30) REVERT: D 56 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8409 (mt-10) REVERT: F 42 GLU cc_start: 0.8644 (tm-30) cc_final: 0.7780 (tm-30) REVERT: H 26 ARG cc_start: 0.7747 (mmm160) cc_final: 0.7159 (mmm160) REVERT: H 42 GLU cc_start: 0.8743 (tm-30) cc_final: 0.7981 (tm-30) REVERT: H 56 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8418 (mt-10) outliers start: 24 outliers final: 19 residues processed: 189 average time/residue: 0.3898 time to fit residues: 98.3442 Evaluate side-chains 183 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 2.348 ------------------------------------------------------------------------------- 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 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 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 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: 3.9990 chunk 39 optimal weight: 0.0670 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 85 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.192134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.146596 restraints weight = 9412.586| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.96 r_work: 0.3405 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9816 Z= 0.127 Angle : 0.599 10.641 13386 Z= 0.278 Chirality : 0.039 0.155 1508 Planarity : 0.005 0.056 1676 Dihedral : 15.080 79.200 1840 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.90 % Allowed : 19.10 % Favored : 80.00 % 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: 1.40 (0.23), residues: 568 sheet: -0.17 (0.32), residues: 192 loop : -0.40 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS A 2 PHE 0.008 0.002 PHE E 137 TYR 0.011 0.002 TYR G 128 ARG 0.014 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 506) hydrogen bonds : angle 4.59654 ( 1518) metal coordination : bond 0.00772 ( 32) metal coordination : angle 5.02494 ( 48) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00270 ( 9784) covalent geometry : angle 0.51931 (13336) *********************** 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 169 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 2.135 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7336 (ttm170) cc_final: 0.6855 (tmt170) REVERT: C 1 MET cc_start: 0.7902 (ptp) cc_final: 0.7475 (ptp) REVERT: C 17 ARG cc_start: 0.7209 (ttm110) cc_final: 0.6831 (tmm160) REVERT: C 25 ILE cc_start: 0.8918 (mt) cc_final: 0.8568 (mm) REVERT: C 42 GLU cc_start: 0.7912 (tt0) cc_final: 0.7697 (pt0) REVERT: E 1 MET cc_start: 0.7928 (ptp) cc_final: 0.7558 (ptp) REVERT: E 17 ARG cc_start: 0.7254 (ttm110) cc_final: 0.6894 (tmt170) REVERT: E 25 ILE cc_start: 0.8954 (mt) cc_final: 0.8628 (mm) REVERT: E 42 GLU cc_start: 0.7727 (tt0) cc_final: 0.7501 (tt0) REVERT: G 1 MET cc_start: 0.7810 (ptp) cc_final: 0.7572 (ptp) REVERT: B 26 ARG cc_start: 0.7709 (mmm160) cc_final: 0.7423 (mmm160) REVERT: B 42 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7173 (tm-30) REVERT: D 42 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8162 (tm-30) REVERT: F 26 ARG cc_start: 0.7562 (mmm-85) cc_final: 0.6985 (mmm160) REVERT: F 42 GLU cc_start: 0.8482 (tm-30) cc_final: 0.7549 (tm-30) REVERT: H 26 ARG cc_start: 0.7690 (mmm160) cc_final: 0.7363 (mmm160) REVERT: H 42 GLU cc_start: 0.8566 (tm-30) cc_final: 0.7870 (tm-30) outliers start: 9 outliers final: 7 residues processed: 164 average time/residue: 0.4300 time to fit residues: 96.6920 Evaluate side-chains 166 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain H residue 43 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: 1.9990 chunk 7 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.191801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.146065 restraints weight = 9544.541| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.96 r_work: 0.3385 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 0.022 9816 Z= 0.153 Angle : 0.605 10.004 13386 Z= 0.279 Chirality : 0.039 0.150 1508 Planarity : 0.005 0.051 1676 Dihedral : 14.769 76.732 1840 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.00 % Allowed : 19.40 % 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 (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: 0.78 (0.25), residues: 1160 helix: 1.48 (0.22), residues: 576 sheet: -0.09 (0.31), residues: 192 loop : -0.51 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS A 2 PHE 0.010 0.002 PHE E 124 TYR 0.017 0.002 TYR G 121 ARG 0.008 0.000 ARG F 7 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 506) hydrogen bonds : angle 4.58634 ( 1518) metal coordination : bond 0.00840 ( 32) metal coordination : angle 5.02614 ( 48) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00341 ( 9784) covalent geometry : angle 0.52552 (13336) *********************** 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 167 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7309 (ttm170) cc_final: 0.6859 (tmt170) REVERT: C 1 MET cc_start: 0.7905 (ptp) cc_final: 0.7486 (ptp) REVERT: C 17 ARG cc_start: 0.7230 (ttm110) cc_final: 0.6865 (tmm160) REVERT: C 25 ILE cc_start: 0.8921 (mt) cc_final: 0.8576 (mm) REVERT: C 42 GLU cc_start: 0.7898 (tt0) cc_final: 0.7671 (pt0) REVERT: E 1 MET cc_start: 0.7954 (ptp) cc_final: 0.7579 (ptp) REVERT: E 17 ARG cc_start: 0.7299 (ttm110) cc_final: 0.6847 (tmm160) REVERT: E 25 ILE cc_start: 0.8961 (mt) cc_final: 0.8634 (mm) REVERT: E 42 GLU cc_start: 0.7763 (tt0) cc_final: 0.7536 (tt0) REVERT: G 1 MET cc_start: 0.7856 (ptp) cc_final: 0.7622 (ptp) REVERT: G 17 ARG cc_start: 0.7404 (ttm110) cc_final: 0.7086 (tmt170) REVERT: G 87 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7632 (ttm170) REVERT: B 42 GLU cc_start: 0.8479 (tm-30) cc_final: 0.7293 (tm-30) REVERT: D 42 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7791 (tm-30) REVERT: F 26 ARG cc_start: 0.7565 (mmm-85) cc_final: 0.6993 (mmm160) REVERT: F 42 GLU cc_start: 0.8499 (tm-30) cc_final: 0.7632 (tm-30) REVERT: H 26 ARG cc_start: 0.7694 (mmm160) cc_final: 0.7318 (mmm160) REVERT: H 42 GLU cc_start: 0.8578 (tm-30) cc_final: 0.7845 (tm-30) outliers start: 10 outliers final: 7 residues processed: 163 average time/residue: 0.4462 time to fit residues: 101.2356 Evaluate side-chains 163 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 E residue 61 THR Chi-restraints excluded: chain G residue 87 ARG 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 62 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 95 optimal weight: 0.3980 chunk 28 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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 = 0.4046 r_free = 0.4046 target = 0.186915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.139795 restraints weight = 9482.197| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.97 r_work: 0.3320 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9816 Z= 0.231 Angle : 0.652 9.972 13386 Z= 0.302 Chirality : 0.040 0.150 1508 Planarity : 0.005 0.052 1676 Dihedral : 14.854 84.873 1840 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.40 % Allowed : 19.40 % 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: 0.70 (0.25), residues: 1160 helix: 1.33 (0.23), residues: 580 sheet: 0.03 (0.31), residues: 172 loop : -0.49 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS A 2 PHE 0.015 0.002 PHE E 124 TYR 0.020 0.002 TYR C 121 ARG 0.008 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 506) hydrogen bonds : angle 4.79760 ( 1518) metal coordination : bond 0.01069 ( 32) metal coordination : angle 5.14737 ( 48) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00538 ( 9784) covalent geometry : angle 0.57600 (13336) *********************** 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 170 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7332 (ttm170) cc_final: 0.6867 (tmt170) REVERT: C 1 MET cc_start: 0.8138 (ptp) cc_final: 0.7884 (ptp) REVERT: C 17 ARG cc_start: 0.7249 (ttm110) cc_final: 0.6862 (tmm160) REVERT: C 25 ILE cc_start: 0.8932 (mt) cc_final: 0.8545 (mm) REVERT: C 42 GLU cc_start: 0.7993 (tt0) cc_final: 0.7661 (pt0) REVERT: E 1 MET cc_start: 0.8155 (ptp) cc_final: 0.7723 (ptp) REVERT: E 17 ARG cc_start: 0.7317 (ttm110) cc_final: 0.6855 (tmm160) REVERT: E 25 ILE cc_start: 0.8971 (mt) cc_final: 0.8642 (mm) REVERT: E 42 GLU cc_start: 0.7856 (tt0) cc_final: 0.7626 (tt0) REVERT: G 1 MET cc_start: 0.7987 (ptp) cc_final: 0.7756 (ptp) REVERT: G 17 ARG cc_start: 0.7428 (ttm110) cc_final: 0.7080 (tmt170) REVERT: G 42 GLU cc_start: 0.8030 (tt0) cc_final: 0.7618 (pt0) REVERT: G 87 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7627 (ttm170) REVERT: B 42 GLU cc_start: 0.8540 (tm-30) cc_final: 0.7705 (tm-30) REVERT: D 42 GLU cc_start: 0.8525 (tt0) cc_final: 0.7727 (tm-30) REVERT: F 26 ARG cc_start: 0.7568 (mmm-85) cc_final: 0.6991 (mmm160) REVERT: F 42 GLU cc_start: 0.8554 (tm-30) cc_final: 0.7659 (tm-30) REVERT: H 26 ARG cc_start: 0.7750 (mmm160) cc_final: 0.7319 (mmm160) REVERT: H 42 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8033 (tm-30) outliers start: 14 outliers final: 12 residues processed: 161 average time/residue: 0.2683 time to fit residues: 57.9742 Evaluate side-chains 168 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 E residue 44 CYS Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 87 ARG 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 F residue 40 THR 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: 9.9990 chunk 13 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 56 optimal weight: 0.0170 chunk 46 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 overall best weight: 0.7220 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.190257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.143375 restraints weight = 9429.285| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.04 r_work: 0.3386 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3075 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= 0.132 Angle : 0.606 10.072 13386 Z= 0.279 Chirality : 0.039 0.169 1508 Planarity : 0.004 0.052 1676 Dihedral : 13.936 88.822 1840 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.00 % Allowed : 19.90 % 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: 0.90 (0.25), residues: 1160 helix: 1.41 (0.23), residues: 572 sheet: 0.31 (0.32), residues: 168 loop : -0.32 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS A 2 PHE 0.010 0.002 PHE B 38 TYR 0.017 0.002 TYR G 121 ARG 0.008 0.000 ARG F 7 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 506) hydrogen bonds : angle 4.54263 ( 1518) metal coordination : bond 0.00759 ( 32) metal coordination : angle 5.09528 ( 48) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00284 ( 9784) covalent geometry : angle 0.52490 (13336) *********************** 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 165 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7305 (ttm170) cc_final: 0.6917 (tmt170) REVERT: C 1 MET cc_start: 0.7851 (ptp) cc_final: 0.7472 (ptp) REVERT: C 17 ARG cc_start: 0.7217 (ttm110) cc_final: 0.6985 (tmt170) REVERT: C 25 ILE cc_start: 0.8947 (mt) cc_final: 0.8570 (mm) REVERT: C 42 GLU cc_start: 0.7964 (tt0) cc_final: 0.7761 (pt0) REVERT: C 43 THR cc_start: 0.8196 (m) cc_final: 0.7854 (p) REVERT: E 1 MET cc_start: 0.7967 (ptp) cc_final: 0.7603 (ptp) REVERT: E 17 ARG cc_start: 0.7345 (ttm110) cc_final: 0.6924 (tmm160) REVERT: E 25 ILE cc_start: 0.8997 (mt) cc_final: 0.8707 (mm) REVERT: E 42 GLU cc_start: 0.7761 (tt0) cc_final: 0.7541 (tt0) REVERT: G 1 MET cc_start: 0.7796 (ptp) cc_final: 0.7450 (ptp) REVERT: G 17 ARG cc_start: 0.7430 (ttm110) cc_final: 0.7143 (tmt170) REVERT: G 87 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7632 (ttm170) REVERT: B 42 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7277 (tm-30) REVERT: D 42 GLU cc_start: 0.8441 (tt0) cc_final: 0.7618 (tm-30) REVERT: F 26 ARG cc_start: 0.7578 (mmm-85) cc_final: 0.7026 (mmm160) REVERT: F 42 GLU cc_start: 0.8461 (tm-30) cc_final: 0.7447 (tm-30) REVERT: H 26 ARG cc_start: 0.7726 (mmm160) cc_final: 0.7319 (mmm160) REVERT: H 42 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8006 (tm-30) outliers start: 10 outliers final: 8 residues processed: 162 average time/residue: 0.2352 time to fit residues: 52.4428 Evaluate side-chains 160 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 E residue 61 THR Chi-restraints excluded: chain G residue 44 CYS Chi-restraints excluded: chain G residue 87 ARG 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 20 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.185322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.137834 restraints weight = 9445.247| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.95 r_work: 0.3298 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9816 Z= 0.273 Angle : 0.695 10.248 13386 Z= 0.322 Chirality : 0.042 0.156 1508 Planarity : 0.005 0.051 1676 Dihedral : 14.420 87.487 1840 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.00 % Allowed : 20.10 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.64 (0.25), residues: 1160 helix: 1.25 (0.22), residues: 584 sheet: -0.02 (0.31), residues: 172 loop : -0.48 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS A 2 PHE 0.016 0.002 PHE E 124 TYR 0.020 0.003 TYR G 121 ARG 0.010 0.001 ARG D 7 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 506) hydrogen bonds : angle 4.89011 ( 1518) metal coordination : bond 0.01129 ( 32) metal coordination : angle 5.24376 ( 48) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00638 ( 9784) covalent geometry : angle 0.62112 (13336) ********************** 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 173 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7297 (ttm170) cc_final: 0.6851 (tmt170) REVERT: C 1 MET cc_start: 0.8124 (ptp) cc_final: 0.7860 (ptp) REVERT: C 17 ARG cc_start: 0.7241 (ttm110) cc_final: 0.6836 (tmm160) REVERT: C 25 ILE cc_start: 0.8954 (mt) cc_final: 0.8575 (mm) REVERT: C 42 GLU cc_start: 0.7996 (tt0) cc_final: 0.7634 (pt0) REVERT: E 1 MET cc_start: 0.8213 (ptp) cc_final: 0.7810 (ptp) REVERT: E 17 ARG cc_start: 0.7302 (ttm110) cc_final: 0.6844 (tmm160) REVERT: E 25 ILE cc_start: 0.8983 (mt) cc_final: 0.8690 (mm) REVERT: E 42 GLU cc_start: 0.7877 (tt0) cc_final: 0.7625 (tt0) REVERT: G 1 MET cc_start: 0.8033 (ptp) cc_final: 0.7786 (ptp) REVERT: G 17 ARG cc_start: 0.7464 (ttm110) cc_final: 0.7053 (tmt170) REVERT: G 25 ILE cc_start: 0.9045 (mp) cc_final: 0.8591 (mm) REVERT: G 42 GLU cc_start: 0.8040 (tt0) cc_final: 0.7660 (pt0) REVERT: B 42 GLU cc_start: 0.8586 (tm-30) cc_final: 0.7791 (tm-30) REVERT: D 42 GLU cc_start: 0.8552 (tt0) cc_final: 0.7695 (tm-30) REVERT: F 26 ARG cc_start: 0.7557 (mmm-85) cc_final: 0.6987 (mmm160) REVERT: F 42 GLU cc_start: 0.8572 (tm-30) cc_final: 0.7711 (tm-30) REVERT: H 26 ARG cc_start: 0.7767 (mmm160) cc_final: 0.7314 (mmm160) REVERT: H 42 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8116 (tm-30) outliers start: 10 outliers final: 9 residues processed: 168 average time/residue: 0.2506 time to fit residues: 56.6985 Evaluate side-chains 166 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 E residue 61 THR 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 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: 0.9990 chunk 65 optimal weight: 0.0670 chunk 77 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 53 optimal weight: 0.0270 chunk 63 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.190211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.143381 restraints weight = 9452.002| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.02 r_work: 0.3381 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9816 Z= 0.130 Angle : 0.624 10.767 13386 Z= 0.286 Chirality : 0.039 0.171 1508 Planarity : 0.004 0.055 1676 Dihedral : 13.608 86.634 1840 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.70 % Allowed : 20.20 % 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: 0.90 (0.25), residues: 1160 helix: 1.37 (0.23), residues: 572 sheet: 0.31 (0.31), residues: 168 loop : -0.25 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS A 2 PHE 0.008 0.002 PHE G 137 TYR 0.018 0.002 TYR G 121 ARG 0.009 0.000 ARG B 7 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 506) hydrogen bonds : angle 4.55421 ( 1518) metal coordination : bond 0.00749 ( 32) metal coordination : angle 5.15600 ( 48) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00277 ( 9784) covalent geometry : angle 0.54285 (13336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6255.00 seconds wall clock time: 112 minutes 45.50 seconds (6765.50 seconds total)