Starting phenix.real_space_refine on Wed Mar 4 11:27:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sk4_25172/03_2026/7sk4_25172_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sk4_25172/03_2026/7sk4_25172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sk4_25172/03_2026/7sk4_25172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sk4_25172/03_2026/7sk4_25172.map" model { file = "/net/cci-nas-00/data/ceres_data/7sk4_25172/03_2026/7sk4_25172_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sk4_25172/03_2026/7sk4_25172_trim.cif" } resolution = 3.3 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= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 37 5.16 5 C 4330 2.51 5 N 1084 2.21 5 O 1205 1.98 5 H 6489 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 13145 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 4995 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 11, 'TRANS': 293} Chain: "B" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1171 Classifications: {'peptide': 69} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "C" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1615 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1913 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "E" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1533 Classifications: {'peptide': 101} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "F" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1862 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.53, per 1000 atoms: 0.19 Number of scatterers: 13145 At special positions: 0 Unit cell: (66.96, 77.76, 149.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 O 1205 8.00 N 1084 7.00 C 4330 6.00 H 6489 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 34 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 50 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.04 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.03 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: 1.13 Conformation dependent library (CDL) restraints added in 437.1 milliseconds 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1570 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 17 sheets defined 34.3% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 39 through 76 removed outlier: 3.808A pdb=" N PHE A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR A 75 " --> pdb=" O GLN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.635A pdb=" N LEU A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 106 removed outlier: 3.817A pdb=" N TRP A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 148 removed outlier: 3.924A pdb=" N TYR A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 152 Processing helix chain 'A' and resid 153 through 182 Proline residue: A 178 - end of helix removed outlier: 3.731A pdb=" N TYR A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 218 Processing helix chain 'A' and resid 221 through 242 removed outlier: 3.638A pdb=" N LEU A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.808A pdb=" N HIS A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 280 removed outlier: 4.095A pdb=" N PHE A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 286 through 316 removed outlier: 3.844A pdb=" N HIS A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N CYS A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Proline residue: A 312 - end of helix Processing helix chain 'A' and resid 319 through 331 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.555A pdb=" N VAL B 23 " --> pdb=" O ARG B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 67 Processing helix chain 'D' and resid 31 through 34 Processing helix chain 'D' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 removed outlier: 4.020A pdb=" N SER F 112 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 187 Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 8 Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.806A pdb=" N LEU C 12 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.806A pdb=" N LEU C 12 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR C 98 " --> pdb=" O GLN C 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AA8, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.549A pdb=" N MET D 86 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 14 through 15 removed outlier: 5.921A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 14 through 15 removed outlier: 4.208A pdb=" N TYR D 117 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AB3, first strand: chain 'E' and resid 36 through 38 removed outlier: 6.730A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 86 through 87 removed outlier: 4.178A pdb=" N TYR E 87 " --> pdb=" O THR E 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 90 through 91 removed outlier: 3.743A pdb=" N THR E 98 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 6 through 10 Processing sheet with id=AB7, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.744A pdb=" N ALA F 52 " --> pdb=" O TRP F 39 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.962A pdb=" N TYR F 119 " --> pdb=" O ARG F 101 " (cutoff:3.500A) 335 hydrogen bonds defined for protein. 903 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: 3.03 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6479 1.03 - 1.23: 13 1.23 - 1.42: 2994 1.42 - 1.62: 3796 1.62 - 1.81: 50 Bond restraints: 13332 Sorted by residual: bond pdb=" C6 CLR A 401 " pdb=" C7 CLR A 401 " ideal model delta sigma weight residual 1.492 1.539 -0.047 2.00e-02 2.50e+03 5.53e+00 bond pdb=" C6 CLR A 402 " pdb=" C7 CLR A 402 " ideal model delta sigma weight residual 1.492 1.539 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" C20 CLR A 402 " pdb=" C22 CLR A 402 " ideal model delta sigma weight residual 1.535 1.576 -0.041 2.00e-02 2.50e+03 4.17e+00 bond pdb=" C13 CLR A 401 " pdb=" C14 CLR A 401 " ideal model delta sigma weight residual 1.537 1.578 -0.041 2.00e-02 2.50e+03 4.11e+00 bond pdb=" C13 CLR A 402 " pdb=" C14 CLR A 402 " ideal model delta sigma weight residual 1.537 1.577 -0.040 2.00e-02 2.50e+03 4.03e+00 ... (remaining 13327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 23735 1.62 - 3.24: 165 3.24 - 4.86: 32 4.86 - 6.48: 6 6.48 - 8.09: 2 Bond angle restraints: 23940 Sorted by residual: angle pdb=" C22 CLR A 401 " pdb=" C23 CLR A 401 " pdb=" C24 CLR A 401 " ideal model delta sigma weight residual 111.95 103.86 8.09 3.00e+00 1.11e-01 7.28e+00 angle pdb=" C22 CLR A 402 " pdb=" C23 CLR A 402 " pdb=" C24 CLR A 402 " ideal model delta sigma weight residual 111.95 104.04 7.91 3.00e+00 1.11e-01 6.95e+00 angle pdb=" C23 CLR A 402 " pdb=" C24 CLR A 402 " pdb=" C25 CLR A 402 " ideal model delta sigma weight residual 115.14 108.71 6.43 3.00e+00 1.11e-01 4.59e+00 angle pdb=" C23 CLR A 401 " pdb=" C24 CLR A 401 " pdb=" C25 CLR A 401 " ideal model delta sigma weight residual 115.14 109.01 6.13 3.00e+00 1.11e-01 4.17e+00 angle pdb=" C17 CLR A 401 " pdb=" C20 CLR A 401 " pdb=" C22 CLR A 401 " ideal model delta sigma weight residual 109.45 103.60 5.85 3.00e+00 1.11e-01 3.81e+00 ... (remaining 23935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 5892 17.74 - 35.48: 449 35.48 - 53.22: 111 53.22 - 70.96: 29 70.96 - 88.70: 7 Dihedral angle restraints: 6488 sinusoidal: 3434 harmonic: 3054 Sorted by residual: dihedral pdb=" CB CYS F 25 " pdb=" SG CYS F 25 " pdb=" SG CYS F 99 " pdb=" CB CYS F 99 " ideal model delta sinusoidal sigma weight residual 93.00 61.76 31.24 1 1.00e+01 1.00e-02 1.39e+01 dihedral pdb=" CA THR A 147 " pdb=" C THR A 147 " pdb=" N TYR A 148 " pdb=" CA TYR A 148 " ideal model delta harmonic sigma weight residual -180.00 -164.02 -15.98 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA PRO A 38 " pdb=" C PRO A 38 " pdb=" N ASN A 39 " pdb=" CA ASN A 39 " ideal model delta harmonic sigma weight residual 180.00 -164.63 -15.37 0 5.00e+00 4.00e-02 9.45e+00 ... (remaining 6485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 954 0.071 - 0.142: 86 0.142 - 0.212: 1 0.212 - 0.283: 2 0.283 - 0.354: 6 Chirality restraints: 1049 Sorted by residual: chirality pdb=" C17 CLR A 401 " pdb=" C13 CLR A 401 " pdb=" C16 CLR A 401 " pdb=" C20 CLR A 401 " both_signs ideal model delta sigma weight residual False 2.55 2.91 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C17 CLR A 402 " pdb=" C13 CLR A 402 " pdb=" C16 CLR A 402 " pdb=" C20 CLR A 402 " both_signs ideal model delta sigma weight residual False 2.55 2.90 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C20 CLR A 401 " pdb=" C17 CLR A 401 " pdb=" C21 CLR A 401 " pdb=" C22 CLR A 401 " both_signs ideal model delta sigma weight residual False 2.59 2.91 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 1046 not shown) Planarity restraints: 1926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 40 " -0.017 5.00e-02 4.00e+02 2.52e-02 1.01e+00 pdb=" N PRO C 41 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 34 " 0.016 5.00e-02 4.00e+02 2.40e-02 9.23e-01 pdb=" N PRO A 35 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 35 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 35 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 272 " 0.005 2.00e-02 2.50e+03 9.22e-03 8.50e-01 pdb=" C VAL A 272 " -0.016 2.00e-02 2.50e+03 pdb=" O VAL A 272 " 0.006 2.00e-02 2.50e+03 pdb=" N LEU A 273 " 0.005 2.00e-02 2.50e+03 ... (remaining 1923 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 589 2.19 - 2.79: 26100 2.79 - 3.39: 35305 3.39 - 4.00: 46629 4.00 - 4.60: 72121 Nonbonded interactions: 180744 Sorted by model distance: nonbonded pdb=" OE1 GLU C 82 " pdb=" H GLU C 82 " model vdw 1.585 2.450 nonbonded pdb=" O VAL A 217 " pdb=" H PHE A 221 " model vdw 1.602 2.450 nonbonded pdb="HH22 ARG D 70 " pdb=" OD1 ASP D 93 " model vdw 1.613 2.450 nonbonded pdb=" H ARG D 90 " pdb=" OD2 ASP D 93 " model vdw 1.666 2.450 nonbonded pdb=" O ILE A 123 " pdb="HD22 ASN A 127 " model vdw 1.668 2.450 ... (remaining 180739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 3 through 13 or resid 18 through 91 or resid 93 through 94 \ or resid 98 through 106)) selection = (chain 'E' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG \ 13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13 \ )) or resid 4 through 91 or resid 93 through 94 or resid 98 through 106)) } ncs_group { reference = (chain 'D' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2)) or resid 6 through 31 or resid 33 or resid 35 through 5 \ 2 or resid 54 or resid 57 through 88 or (resid 89 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name HB \ 2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 90 through 102 or resid 105 through 106 or res \ id 111 or resid 113 or resid 116 through 127)) selection = (chain 'F' and (resid 5 through 31 or resid 33 or resid 35 through 52 or resid 5 \ 4 or resid 57 through 102 or resid 105 or resid 109 or resid 114 or resid 116 or \ resid 118 through 129)) } 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: 6.200 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: 0.080 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.250 Find NCS groups from input model: 0.110 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 : 0.003 0.047 6850 Z= 0.148 Angle : 0.503 8.094 9343 Z= 0.241 Chirality : 0.048 0.354 1049 Planarity : 0.002 0.025 1135 Dihedral : 14.269 88.702 2499 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.26 (0.30), residues: 817 helix: 2.23 (0.33), residues: 246 sheet: -0.92 (0.34), residues: 236 loop : -1.44 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 19 TYR 0.010 0.001 TYR E 50 PHE 0.007 0.001 PHE F 30 TRP 0.009 0.001 TRP F 109 HIS 0.002 0.001 HIS B 2 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6843) covalent geometry : angle 0.50280 ( 9329) SS BOND : bond 0.00280 ( 7) SS BOND : angle 0.70650 ( 14) hydrogen bonds : bond 0.16700 ( 322) hydrogen bonds : angle 6.76548 ( 903) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7580 (t80) cc_final: 0.7218 (t80) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2125 time to fit residues: 26.7677 Evaluate side-chains 77 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.093513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.085625 restraints weight = 47772.730| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.44 r_work: 0.3401 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6850 Z= 0.127 Angle : 0.495 4.261 9343 Z= 0.266 Chirality : 0.040 0.149 1049 Planarity : 0.003 0.028 1135 Dihedral : 5.072 53.899 1048 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.27 % Allowed : 5.34 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.14 (0.30), residues: 817 helix: 2.54 (0.32), residues: 246 sheet: -0.79 (0.34), residues: 236 loop : -1.59 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 101 TYR 0.011 0.001 TYR D 53 PHE 0.008 0.001 PHE C 99 TRP 0.008 0.001 TRP D 39 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6843) covalent geometry : angle 0.49514 ( 9329) SS BOND : bond 0.00388 ( 7) SS BOND : angle 0.49443 ( 14) hydrogen bonds : bond 0.05251 ( 322) hydrogen bonds : angle 5.38223 ( 903) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7638 (t80) cc_final: 0.7301 (t80) REVERT: C 28 GLN cc_start: 0.7410 (mp10) cc_final: 0.7099 (mp-120) REVERT: D 9 GLU cc_start: 0.8010 (mp0) cc_final: 0.7777 (mp0) outliers start: 2 outliers final: 1 residues processed: 87 average time/residue: 0.1865 time to fit residues: 21.8755 Evaluate side-chains 82 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 78 optimal weight: 0.2980 chunk 52 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.091984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.084096 restraints weight = 48765.052| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.44 r_work: 0.3371 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6850 Z= 0.191 Angle : 0.516 4.748 9343 Z= 0.279 Chirality : 0.040 0.146 1049 Planarity : 0.003 0.030 1135 Dihedral : 5.106 50.533 1048 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.82 % Allowed : 6.57 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.30 (0.30), residues: 817 helix: 2.46 (0.31), residues: 246 sheet: -0.92 (0.34), residues: 234 loop : -1.70 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 101 TYR 0.014 0.001 TYR C 92 PHE 0.008 0.001 PHE F 30 TRP 0.007 0.001 TRP A 208 HIS 0.004 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 6843) covalent geometry : angle 0.51619 ( 9329) SS BOND : bond 0.00541 ( 7) SS BOND : angle 0.56070 ( 14) hydrogen bonds : bond 0.05235 ( 322) hydrogen bonds : angle 5.24056 ( 903) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7728 (t80) cc_final: 0.7368 (t80) REVERT: D 9 GLU cc_start: 0.8101 (mp0) cc_final: 0.7828 (mp0) outliers start: 6 outliers final: 6 residues processed: 89 average time/residue: 0.2054 time to fit residues: 24.1951 Evaluate side-chains 87 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 61 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.0770 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.092362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.084378 restraints weight = 48487.030| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.45 r_work: 0.3380 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6850 Z= 0.169 Angle : 0.505 4.818 9343 Z= 0.271 Chirality : 0.040 0.146 1049 Planarity : 0.003 0.030 1135 Dihedral : 4.976 47.333 1048 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.09 % Allowed : 8.07 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.31 (0.30), residues: 817 helix: 2.52 (0.32), residues: 246 sheet: -0.97 (0.34), residues: 234 loop : -1.73 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 101 TYR 0.013 0.001 TYR C 92 PHE 0.008 0.001 PHE A 124 TRP 0.006 0.001 TRP A 265 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6843) covalent geometry : angle 0.50464 ( 9329) SS BOND : bond 0.00473 ( 7) SS BOND : angle 0.54827 ( 14) hydrogen bonds : bond 0.04902 ( 322) hydrogen bonds : angle 5.06623 ( 903) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7675 (t80) cc_final: 0.7338 (t80) REVERT: B 34 CYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6876 (m) REVERT: D 9 GLU cc_start: 0.8074 (mp0) cc_final: 0.7809 (mp0) outliers start: 8 outliers final: 6 residues processed: 91 average time/residue: 0.2165 time to fit residues: 26.0833 Evaluate side-chains 88 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 61 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 63 optimal weight: 0.0670 chunk 21 optimal weight: 2.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.092178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.084187 restraints weight = 48811.036| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.45 r_work: 0.3374 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6850 Z= 0.167 Angle : 0.503 4.838 9343 Z= 0.270 Chirality : 0.040 0.145 1049 Planarity : 0.003 0.031 1135 Dihedral : 4.865 42.717 1048 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.09 % Allowed : 9.71 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.33 (0.30), residues: 817 helix: 2.51 (0.32), residues: 247 sheet: -1.00 (0.34), residues: 232 loop : -1.75 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 1 TYR 0.013 0.001 TYR C 92 PHE 0.008 0.001 PHE A 124 TRP 0.007 0.001 TRP A 265 HIS 0.004 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 6843) covalent geometry : angle 0.50262 ( 9329) SS BOND : bond 0.00445 ( 7) SS BOND : angle 0.67593 ( 14) hydrogen bonds : bond 0.04811 ( 322) hydrogen bonds : angle 4.98790 ( 903) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7699 (t80) cc_final: 0.7368 (t80) REVERT: D 9 GLU cc_start: 0.8052 (mp0) cc_final: 0.7794 (mp0) outliers start: 8 outliers final: 6 residues processed: 86 average time/residue: 0.2118 time to fit residues: 23.8806 Evaluate side-chains 85 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 61 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.092435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.084484 restraints weight = 48838.205| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.45 r_work: 0.3380 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6850 Z= 0.158 Angle : 0.507 5.024 9343 Z= 0.270 Chirality : 0.040 0.145 1049 Planarity : 0.003 0.031 1135 Dihedral : 4.742 36.415 1048 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.09 % Allowed : 11.35 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.27 (0.30), residues: 817 helix: 2.57 (0.32), residues: 247 sheet: -0.97 (0.34), residues: 232 loop : -1.72 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 1 TYR 0.012 0.001 TYR C 92 PHE 0.008 0.001 PHE A 124 TRP 0.007 0.001 TRP A 265 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6843) covalent geometry : angle 0.50664 ( 9329) SS BOND : bond 0.00448 ( 7) SS BOND : angle 0.89881 ( 14) hydrogen bonds : bond 0.04696 ( 322) hydrogen bonds : angle 4.90571 ( 903) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7663 (t80) cc_final: 0.7343 (t80) REVERT: D 9 GLU cc_start: 0.8037 (mp0) cc_final: 0.7791 (mp0) outliers start: 8 outliers final: 8 residues processed: 85 average time/residue: 0.1966 time to fit residues: 22.5533 Evaluate side-chains 87 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain D residue 53 TYR Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 61 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.092616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.084644 restraints weight = 48405.802| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.44 r_work: 0.3387 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6850 Z= 0.142 Angle : 0.487 4.679 9343 Z= 0.261 Chirality : 0.040 0.144 1049 Planarity : 0.003 0.031 1135 Dihedral : 4.582 36.397 1048 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.09 % Allowed : 11.76 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.19 (0.30), residues: 817 helix: 2.67 (0.32), residues: 247 sheet: -0.95 (0.34), residues: 232 loop : -1.68 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 1 TYR 0.011 0.001 TYR C 92 PHE 0.008 0.001 PHE A 124 TRP 0.007 0.001 TRP A 265 HIS 0.003 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6843) covalent geometry : angle 0.48685 ( 9329) SS BOND : bond 0.00418 ( 7) SS BOND : angle 0.81105 ( 14) hydrogen bonds : bond 0.04542 ( 322) hydrogen bonds : angle 4.81334 ( 903) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7635 (tpp) cc_final: 0.7212 (mmp) REVERT: A 49 PHE cc_start: 0.7668 (t80) cc_final: 0.7353 (t80) REVERT: D 9 GLU cc_start: 0.8027 (mp0) cc_final: 0.7779 (mp0) outliers start: 8 outliers final: 7 residues processed: 84 average time/residue: 0.1794 time to fit residues: 20.5003 Evaluate side-chains 84 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain F residue 14 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 78 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.092405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.084481 restraints weight = 48190.552| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.43 r_work: 0.3384 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6850 Z= 0.155 Angle : 0.501 4.798 9343 Z= 0.268 Chirality : 0.040 0.144 1049 Planarity : 0.003 0.032 1135 Dihedral : 4.602 44.276 1048 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.23 % Allowed : 11.90 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.26 (0.30), residues: 817 helix: 2.61 (0.32), residues: 247 sheet: -0.97 (0.34), residues: 232 loop : -1.73 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 1 TYR 0.012 0.001 TYR C 92 PHE 0.008 0.001 PHE A 124 TRP 0.007 0.001 TRP A 265 HIS 0.005 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6843) covalent geometry : angle 0.50018 ( 9329) SS BOND : bond 0.00449 ( 7) SS BOND : angle 0.78023 ( 14) hydrogen bonds : bond 0.04560 ( 322) hydrogen bonds : angle 4.82864 ( 903) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7647 (t80) cc_final: 0.7332 (t80) outliers start: 9 outliers final: 9 residues processed: 85 average time/residue: 0.1858 time to fit residues: 21.6550 Evaluate side-chains 87 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain D residue 53 TYR Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain F residue 14 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.092851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.084830 restraints weight = 48897.021| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.46 r_work: 0.3388 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6850 Z= 0.141 Angle : 0.492 4.704 9343 Z= 0.263 Chirality : 0.040 0.145 1049 Planarity : 0.003 0.032 1135 Dihedral : 4.596 52.149 1048 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.09 % Allowed : 12.31 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.22 (0.30), residues: 817 helix: 2.67 (0.32), residues: 247 sheet: -0.95 (0.34), residues: 232 loop : -1.72 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 1 TYR 0.011 0.001 TYR C 92 PHE 0.008 0.001 PHE A 124 TRP 0.008 0.001 TRP F 109 HIS 0.003 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6843) covalent geometry : angle 0.49146 ( 9329) SS BOND : bond 0.00440 ( 7) SS BOND : angle 0.73652 ( 14) hydrogen bonds : bond 0.04459 ( 322) hydrogen bonds : angle 4.77874 ( 903) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7660 (t80) cc_final: 0.7347 (t80) outliers start: 8 outliers final: 8 residues processed: 85 average time/residue: 0.1862 time to fit residues: 21.4210 Evaluate side-chains 86 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain D residue 53 TYR Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain F residue 14 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.091279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.083334 restraints weight = 49250.822| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.44 r_work: 0.3360 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6850 Z= 0.218 Angle : 0.556 6.610 9343 Z= 0.298 Chirality : 0.041 0.143 1049 Planarity : 0.004 0.032 1135 Dihedral : 4.838 53.550 1048 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.23 % Allowed : 12.72 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.54 (0.30), residues: 817 helix: 2.44 (0.32), residues: 247 sheet: -1.19 (0.34), residues: 227 loop : -1.90 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 1 TYR 0.015 0.001 TYR C 92 PHE 0.008 0.001 PHE A 134 TRP 0.008 0.001 TRP F 50 HIS 0.005 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 6843) covalent geometry : angle 0.55570 ( 9329) SS BOND : bond 0.00548 ( 7) SS BOND : angle 0.86280 ( 14) hydrogen bonds : bond 0.04836 ( 322) hydrogen bonds : angle 4.98262 ( 903) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7727 (t80) cc_final: 0.7389 (t80) outliers start: 9 outliers final: 9 residues processed: 85 average time/residue: 0.1891 time to fit residues: 21.8426 Evaluate side-chains 86 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain D residue 53 TYR Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain F residue 14 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.092366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.084435 restraints weight = 48417.237| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.42 r_work: 0.3384 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6850 Z= 0.145 Angle : 0.508 5.702 9343 Z= 0.271 Chirality : 0.040 0.144 1049 Planarity : 0.003 0.032 1135 Dihedral : 4.730 57.494 1048 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.23 % Allowed : 12.86 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.32 (0.30), residues: 817 helix: 2.61 (0.32), residues: 247 sheet: -1.03 (0.33), residues: 232 loop : -1.79 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 1 TYR 0.011 0.001 TYR C 92 PHE 0.008 0.001 PHE A 124 TRP 0.007 0.001 TRP F 109 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6843) covalent geometry : angle 0.50789 ( 9329) SS BOND : bond 0.00424 ( 7) SS BOND : angle 0.70215 ( 14) hydrogen bonds : bond 0.04542 ( 322) hydrogen bonds : angle 4.82021 ( 903) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3430.44 seconds wall clock time: 58 minutes 59.47 seconds (3539.47 seconds total)