Starting phenix.real_space_refine on Wed Sep 17 04:49:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ccs_45456/09_2025/9ccs_45456.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ccs_45456/09_2025/9ccs_45456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ccs_45456/09_2025/9ccs_45456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ccs_45456/09_2025/9ccs_45456.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ccs_45456/09_2025/9ccs_45456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ccs_45456/09_2025/9ccs_45456.map" } resolution = 3.17 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= 0.019 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: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2867 2.51 5 N 747 2.21 5 O 902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4530 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1196 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 148} Chain: "B" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1639 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 202} Chain: "C" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1695 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 211} Time building chain proxies: 1.43, per 1000 atoms: 0.32 Number of scatterers: 4530 At special positions: 0 Unit cell: (57.256, 68.202, 122.932, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 902 8.00 N 747 7.00 C 2867 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 44 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 94 " distance=2.04 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 200 " distance=2.04 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 101 " distance=2.04 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 209 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 201.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1104 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 12 sheets defined 8.0% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 37 through 40 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.646A pdb=" N ASP B 88 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 89 " --> pdb=" O ALA B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 89' Processing helix chain 'B' and resid 127 through 133 Processing helix chain 'B' and resid 188 through 195 removed outlier: 3.550A pdb=" N HIS B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 207 removed outlier: 4.192A pdb=" N LEU B 207 " --> pdb=" O HIS B 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 213 through 217 removed outlier: 3.553A pdb=" N ASN C 217 " --> pdb=" O LYS C 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 22 removed outlier: 6.388A pdb=" N PHE A 142 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ARG A 132 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE A 144 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 130 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TRP A 146 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL A 128 " --> pdb=" O TRP A 146 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE A 148 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE A 126 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ALA A 63 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A 128 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLY A 61 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE A 130 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 36 removed outlier: 3.662A pdb=" N LEU A 107 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR A 110 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 72 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.594A pdb=" N ALA A 119 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 154 " --> pdb=" O ALA A 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 11 Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 16 removed outlier: 3.557A pdb=" N THR B 108 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLN B 43 " --> pdb=" O PRO B 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 121 through 124 removed outlier: 5.260A pdb=" N VAL B 139 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU B 185 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU B 141 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N SER B 183 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASN B 143 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU B 181 " --> pdb=" O ASN B 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 153 through 156 Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 11 Processing sheet with id=AB1, first strand: chain 'C' and resid 15 through 16 removed outlier: 7.109A pdb=" N GLU C 15 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR C 120 " --> pdb=" O TYR C 99 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP C 41 " --> pdb=" O ILE C 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 151 through 158 removed outlier: 5.090A pdb=" N GLY C 152 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL C 195 " --> pdb=" O GLY C 152 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEU C 154 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER C 193 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS C 156 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU C 191 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 190 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 166 through 167 removed outlier: 3.990A pdb=" N TYR C 207 " --> pdb=" O VAL C 224 " (cutoff:3.500A) 97 hydrogen bonds defined for protein. 231 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: 0.66 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1421 1.34 - 1.46: 1185 1.46 - 1.58: 2021 1.58 - 1.70: 1 1.70 - 1.82: 17 Bond restraints: 4645 Sorted by residual: bond pdb=" CB PRO C 132 " pdb=" CG PRO C 132 " ideal model delta sigma weight residual 1.492 1.648 -0.156 5.00e-02 4.00e+02 9.72e+00 bond pdb=" N PRO C 132 " pdb=" CA PRO C 132 " ideal model delta sigma weight residual 1.481 1.434 0.047 1.85e-02 2.92e+03 6.44e+00 bond pdb=" CB VAL A 155 " pdb=" CG1 VAL A 155 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.86e+00 bond pdb=" CB TRP B 97 " pdb=" CG TRP B 97 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.05e+00 bond pdb=" CB VAL A 36 " pdb=" CG2 VAL A 36 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.59e+00 ... (remaining 4640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 6210 2.63 - 5.27: 111 5.27 - 7.90: 19 7.90 - 10.54: 2 10.54 - 13.17: 1 Bond angle restraints: 6343 Sorted by residual: angle pdb=" CA PRO C 132 " pdb=" N PRO C 132 " pdb=" CD PRO C 132 " ideal model delta sigma weight residual 112.00 98.83 13.17 1.40e+00 5.10e-01 8.85e+01 angle pdb=" N VAL A 94 " pdb=" CA VAL A 94 " pdb=" C VAL A 94 " ideal model delta sigma weight residual 109.34 118.61 -9.27 2.08e+00 2.31e-01 1.98e+01 angle pdb=" C VAL A 93 " pdb=" N VAL A 94 " pdb=" CA VAL A 94 " ideal model delta sigma weight residual 121.97 129.13 -7.16 1.80e+00 3.09e-01 1.58e+01 angle pdb=" N TYR B 100 " pdb=" CA TYR B 100 " pdb=" C TYR B 100 " ideal model delta sigma weight residual 110.73 116.76 -6.03 1.55e+00 4.16e-01 1.51e+01 angle pdb=" N PRO C 132 " pdb=" CD PRO C 132 " pdb=" CG PRO C 132 " ideal model delta sigma weight residual 103.20 97.75 5.45 1.50e+00 4.44e-01 1.32e+01 ... (remaining 6338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 2324 17.98 - 35.95: 320 35.95 - 53.93: 77 53.93 - 71.90: 16 71.90 - 89.88: 7 Dihedral angle restraints: 2744 sinusoidal: 1013 harmonic: 1731 Sorted by residual: dihedral pdb=" CA TYR B 100 " pdb=" C TYR B 100 " pdb=" N PRO B 101 " pdb=" CA PRO B 101 " ideal model delta harmonic sigma weight residual 180.00 130.03 49.97 0 5.00e+00 4.00e-02 9.99e+01 dihedral pdb=" CB CYS C 27 " pdb=" SG CYS C 27 " pdb=" SG CYS C 101 " pdb=" CB CYS C 101 " ideal model delta sinusoidal sigma weight residual -86.00 -33.75 -52.25 1 1.00e+01 1.00e-02 3.72e+01 dihedral pdb=" CA SER B 12 " pdb=" C SER B 12 " pdb=" N PRO B 13 " pdb=" CA PRO B 13 " ideal model delta harmonic sigma weight residual -180.00 -152.58 -27.42 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 2741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 597 0.068 - 0.137: 111 0.137 - 0.205: 9 0.205 - 0.273: 3 0.273 - 0.342: 1 Chirality restraints: 721 Sorted by residual: chirality pdb=" CB ILE B 26 " pdb=" CA ILE B 26 " pdb=" CG1 ILE B 26 " pdb=" CG2 ILE B 26 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA TYR B 100 " pdb=" N TYR B 100 " pdb=" C TYR B 100 " pdb=" CB TYR B 100 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA VAL A 94 " pdb=" N VAL A 94 " pdb=" C VAL A 94 " pdb=" CB VAL A 94 " both_signs ideal model delta sigma weight residual False 2.44 2.23 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 718 not shown) Planarity restraints: 803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 102 " -0.014 2.00e-02 2.50e+03 2.65e-02 1.75e+01 pdb=" CG TRP B 102 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP B 102 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP B 102 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 102 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TRP B 102 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 102 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 102 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 102 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 102 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 131 " -0.074 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO C 132 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO C 132 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 132 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 100 " 0.054 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO B 101 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 101 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 101 " 0.046 5.00e-02 4.00e+02 ... (remaining 800 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 173 2.69 - 3.24: 4511 3.24 - 3.79: 7853 3.79 - 4.35: 9957 4.35 - 4.90: 16364 Nonbonded interactions: 38858 Sorted by model distance: nonbonded pdb=" OH TYR C 158 " pdb=" OE1 GLU C 161 " model vdw 2.133 3.040 nonbonded pdb=" O TYR A 77 " pdb=" OG SER A 80 " model vdw 2.162 3.040 nonbonded pdb=" OG1 THR C 129 " pdb=" O PHE C 159 " model vdw 2.235 3.040 nonbonded pdb=" OG1 THR A 57 " pdb=" OG1 THR A 90 " model vdw 2.261 3.040 nonbonded pdb=" O SER C 12 " pdb=" OG1 THR C 120 " model vdw 2.264 3.040 ... (remaining 38853 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.000 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 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 : 0.006 0.156 4650 Z= 0.261 Angle : 0.868 13.173 6353 Z= 0.464 Chirality : 0.054 0.342 721 Planarity : 0.008 0.103 803 Dihedral : 17.998 89.878 1625 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.18 % Favored : 87.48 % Rotamer: Outliers : 0.98 % Allowed : 35.03 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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 aren not related in a simple way. whole: -3.26 (0.33), residues: 591 helix: -2.33 (0.85), residues: 16 sheet: -2.16 (0.30), residues: 218 loop : -2.19 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 45 TYR 0.050 0.003 TYR B 100 PHE 0.014 0.003 PHE A 144 TRP 0.057 0.004 TRP B 102 HIS 0.009 0.002 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00616 ( 4645) covalent geometry : angle 0.86621 ( 6343) SS BOND : bond 0.00792 ( 5) SS BOND : angle 1.57221 ( 10) hydrogen bonds : bond 0.18540 ( 97) hydrogen bonds : angle 9.10184 ( 231) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.194 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 76 average time/residue: 0.0510 time to fit residues: 5.4644 Evaluate side-chains 77 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 191 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 48 optimal weight: 0.0870 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.193264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.174852 restraints weight = 6635.491| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 2.98 r_work: 0.4097 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4650 Z= 0.150 Angle : 0.643 7.551 6353 Z= 0.338 Chirality : 0.045 0.149 721 Planarity : 0.006 0.074 803 Dihedral : 6.155 45.518 644 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.83 % Favored : 88.83 % Rotamer: Outliers : 4.31 % Allowed : 32.09 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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 aren not related in a simple way. whole: -3.19 (0.32), residues: 591 helix: -1.65 (0.86), residues: 22 sheet: -2.13 (0.31), residues: 205 loop : -2.18 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 148 TYR 0.018 0.001 TYR B 100 PHE 0.009 0.001 PHE B 104 TRP 0.019 0.002 TRP B 102 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4645) covalent geometry : angle 0.64212 ( 6343) SS BOND : bond 0.00456 ( 5) SS BOND : angle 0.98585 ( 10) hydrogen bonds : bond 0.03838 ( 97) hydrogen bonds : angle 7.80385 ( 231) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.170 Fit side-chains REVERT: B 148 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6630 (tpt90) REVERT: C 121 THR cc_start: 0.7638 (m) cc_final: 0.7410 (p) outliers start: 22 outliers final: 10 residues processed: 86 average time/residue: 0.0466 time to fit residues: 5.9256 Evaluate side-chains 80 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 155 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 2 optimal weight: 0.5980 chunk 1 optimal weight: 0.0670 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.0170 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.194056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.176105 restraints weight = 6612.773| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 2.92 r_work: 0.4097 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4650 Z= 0.149 Angle : 0.630 8.399 6353 Z= 0.327 Chirality : 0.044 0.147 721 Planarity : 0.005 0.073 803 Dihedral : 5.569 41.133 639 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.17 % Favored : 88.49 % Rotamer: Outliers : 5.87 % Allowed : 31.70 % Favored : 62.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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 aren not related in a simple way. whole: -3.02 (0.33), residues: 591 helix: -1.03 (0.99), residues: 22 sheet: -2.06 (0.31), residues: 222 loop : -2.05 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 148 TYR 0.009 0.001 TYR B 55 PHE 0.009 0.001 PHE B 104 TRP 0.013 0.002 TRP B 97 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4645) covalent geometry : angle 0.62969 ( 6343) SS BOND : bond 0.00395 ( 5) SS BOND : angle 0.99680 ( 10) hydrogen bonds : bond 0.03691 ( 97) hydrogen bonds : angle 7.39907 ( 231) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.166 Fit side-chains REVERT: B 148 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6704 (tpt90) REVERT: C 121 THR cc_start: 0.7698 (m) cc_final: 0.7448 (p) outliers start: 30 outliers final: 15 residues processed: 93 average time/residue: 0.0486 time to fit residues: 6.4883 Evaluate side-chains 86 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 190 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.187683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.169736 restraints weight = 6576.953| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 2.85 r_work: 0.4075 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4650 Z= 0.179 Angle : 0.650 9.125 6353 Z= 0.337 Chirality : 0.046 0.252 721 Planarity : 0.005 0.067 803 Dihedral : 5.614 43.141 639 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.17 % Favored : 88.49 % Rotamer: Outliers : 6.07 % Allowed : 31.31 % Favored : 62.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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 aren not related in a simple way. whole: -3.05 (0.33), residues: 591 helix: -0.48 (1.10), residues: 21 sheet: -2.10 (0.30), residues: 225 loop : -2.09 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 148 TYR 0.034 0.002 TYR B 100 PHE 0.008 0.002 PHE C 135 TRP 0.010 0.002 TRP B 41 HIS 0.006 0.002 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 4645) covalent geometry : angle 0.64886 ( 6343) SS BOND : bond 0.00438 ( 5) SS BOND : angle 1.02754 ( 10) hydrogen bonds : bond 0.03700 ( 97) hydrogen bonds : angle 7.29378 ( 231) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.164 Fit side-chains REVERT: B 148 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6603 (tpt90) outliers start: 31 outliers final: 19 residues processed: 91 average time/residue: 0.0530 time to fit residues: 6.7937 Evaluate side-chains 89 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 210 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 55 optimal weight: 0.0770 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.0060 chunk 45 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.195243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.177624 restraints weight = 6607.112| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.93 r_work: 0.4108 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4650 Z= 0.130 Angle : 0.616 6.410 6353 Z= 0.322 Chirality : 0.045 0.251 721 Planarity : 0.005 0.066 803 Dihedral : 5.455 41.982 639 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.81 % Favored : 89.85 % Rotamer: Outliers : 5.09 % Allowed : 32.49 % Favored : 62.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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 aren not related in a simple way. whole: -2.90 (0.34), residues: 591 helix: -0.47 (1.11), residues: 22 sheet: -1.89 (0.32), residues: 222 loop : -2.07 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 148 TYR 0.040 0.001 TYR B 100 PHE 0.010 0.001 PHE B 104 TRP 0.013 0.002 TRP B 97 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4645) covalent geometry : angle 0.61573 ( 6343) SS BOND : bond 0.00324 ( 5) SS BOND : angle 0.84890 ( 10) hydrogen bonds : bond 0.03334 ( 97) hydrogen bonds : angle 7.05822 ( 231) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.164 Fit side-chains REVERT: B 148 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6645 (tpt90) REVERT: C 95 ASP cc_start: 0.6156 (OUTLIER) cc_final: 0.5900 (t0) outliers start: 26 outliers final: 18 residues processed: 89 average time/residue: 0.0447 time to fit residues: 5.8922 Evaluate side-chains 95 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 190 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 38 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 3 optimal weight: 0.0170 chunk 48 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.189341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.171269 restraints weight = 6769.226| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 2.89 r_work: 0.4084 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4650 Z= 0.157 Angle : 0.630 6.697 6353 Z= 0.328 Chirality : 0.046 0.224 721 Planarity : 0.005 0.063 803 Dihedral : 5.487 41.484 639 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.34 % Favored : 88.32 % Rotamer: Outliers : 5.68 % Allowed : 31.31 % Favored : 63.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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 aren not related in a simple way. whole: -2.97 (0.33), residues: 591 helix: -0.19 (1.17), residues: 21 sheet: -1.92 (0.32), residues: 220 loop : -2.15 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 148 TYR 0.031 0.001 TYR B 100 PHE 0.008 0.001 PHE A 144 TRP 0.012 0.002 TRP A 103 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 4645) covalent geometry : angle 0.62945 ( 6343) SS BOND : bond 0.00400 ( 5) SS BOND : angle 0.91256 ( 10) hydrogen bonds : bond 0.03468 ( 97) hydrogen bonds : angle 6.97194 ( 231) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.127 Fit side-chains REVERT: B 148 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6696 (tpt90) REVERT: C 95 ASP cc_start: 0.6167 (OUTLIER) cc_final: 0.5920 (t0) outliers start: 29 outliers final: 18 residues processed: 86 average time/residue: 0.0436 time to fit residues: 5.3429 Evaluate side-chains 92 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 190 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.188234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.169872 restraints weight = 6708.307| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 2.90 r_work: 0.4070 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4650 Z= 0.182 Angle : 0.662 7.909 6353 Z= 0.341 Chirality : 0.047 0.289 721 Planarity : 0.005 0.062 803 Dihedral : 5.612 42.678 639 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.00 % Favored : 88.66 % Rotamer: Outliers : 5.68 % Allowed : 32.29 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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 aren not related in a simple way. whole: -3.00 (0.33), residues: 591 helix: -0.06 (1.20), residues: 21 sheet: -1.92 (0.32), residues: 220 loop : -2.20 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 148 TYR 0.033 0.002 TYR B 100 PHE 0.008 0.001 PHE A 144 TRP 0.025 0.002 TRP A 103 HIS 0.007 0.002 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 4645) covalent geometry : angle 0.66144 ( 6343) SS BOND : bond 0.00455 ( 5) SS BOND : angle 0.96359 ( 10) hydrogen bonds : bond 0.03640 ( 97) hydrogen bonds : angle 6.99408 ( 231) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.165 Fit side-chains REVERT: B 148 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6655 (tpt90) REVERT: C 15 GLU cc_start: 0.5695 (OUTLIER) cc_final: 0.5326 (pp20) REVERT: C 95 ASP cc_start: 0.6190 (OUTLIER) cc_final: 0.5977 (t0) outliers start: 29 outliers final: 20 residues processed: 89 average time/residue: 0.0474 time to fit residues: 6.1893 Evaluate side-chains 94 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 210 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 17 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.186296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.168166 restraints weight = 6682.802| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 2.87 r_work: 0.4054 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4650 Z= 0.208 Angle : 0.688 9.932 6353 Z= 0.354 Chirality : 0.048 0.301 721 Planarity : 0.005 0.061 803 Dihedral : 5.787 44.764 639 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.51 % Favored : 88.16 % Rotamer: Outliers : 5.68 % Allowed : 32.68 % Favored : 61.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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 aren not related in a simple way. whole: -3.12 (0.33), residues: 591 helix: -0.02 (1.21), residues: 21 sheet: -2.13 (0.31), residues: 224 loop : -2.19 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 148 TYR 0.038 0.002 TYR B 100 PHE 0.009 0.002 PHE C 113 TRP 0.028 0.003 TRP A 103 HIS 0.009 0.002 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 4645) covalent geometry : angle 0.68732 ( 6343) SS BOND : bond 0.00517 ( 5) SS BOND : angle 1.12196 ( 10) hydrogen bonds : bond 0.03833 ( 97) hydrogen bonds : angle 7.09956 ( 231) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 67 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: B 59 ASN cc_start: 0.5394 (m110) cc_final: 0.5159 (m110) REVERT: B 148 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6576 (tpt90) REVERT: C 95 ASP cc_start: 0.6199 (OUTLIER) cc_final: 0.5968 (t0) REVERT: C 121 THR cc_start: 0.7803 (m) cc_final: 0.7458 (p) outliers start: 29 outliers final: 24 residues processed: 87 average time/residue: 0.0490 time to fit residues: 6.1002 Evaluate side-chains 92 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 210 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 25 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 55 optimal weight: 0.0570 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.0000 overall best weight: 0.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.193952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.175976 restraints weight = 6655.571| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.97 r_work: 0.4086 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4650 Z= 0.149 Angle : 0.661 8.432 6353 Z= 0.339 Chirality : 0.047 0.293 721 Planarity : 0.005 0.065 803 Dihedral : 5.591 43.290 639 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.17 % Favored : 88.49 % Rotamer: Outliers : 5.28 % Allowed : 33.46 % Favored : 61.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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 aren not related in a simple way. whole: -3.07 (0.33), residues: 591 helix: -0.22 (1.20), residues: 22 sheet: -1.97 (0.33), residues: 211 loop : -2.25 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 148 TYR 0.044 0.002 TYR B 100 PHE 0.009 0.001 PHE B 104 TRP 0.025 0.002 TRP A 103 HIS 0.010 0.002 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4645) covalent geometry : angle 0.66062 ( 6343) SS BOND : bond 0.00468 ( 5) SS BOND : angle 0.99351 ( 10) hydrogen bonds : bond 0.03446 ( 97) hydrogen bonds : angle 6.93109 ( 231) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.176 Fit side-chains REVERT: B 148 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6705 (tpt90) REVERT: B 188 SER cc_start: 0.5466 (OUTLIER) cc_final: 0.4809 (t) REVERT: C 95 ASP cc_start: 0.6111 (OUTLIER) cc_final: 0.5894 (t0) outliers start: 27 outliers final: 22 residues processed: 86 average time/residue: 0.0449 time to fit residues: 5.7011 Evaluate side-chains 92 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 210 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 3 optimal weight: 0.0270 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.187278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.169169 restraints weight = 6591.151| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 2.85 r_work: 0.4066 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4650 Z= 0.207 Angle : 0.709 9.734 6353 Z= 0.364 Chirality : 0.048 0.320 721 Planarity : 0.005 0.063 803 Dihedral : 5.798 43.004 639 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.84 % Favored : 87.82 % Rotamer: Outliers : 5.09 % Allowed : 34.25 % Favored : 60.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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 aren not related in a simple way. whole: -3.13 (0.33), residues: 591 helix: -0.25 (1.18), residues: 22 sheet: -2.10 (0.31), residues: 222 loop : -2.22 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 148 TYR 0.046 0.002 TYR B 100 PHE 0.009 0.002 PHE C 113 TRP 0.034 0.003 TRP A 103 HIS 0.008 0.002 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 4645) covalent geometry : angle 0.70863 ( 6343) SS BOND : bond 0.00536 ( 5) SS BOND : angle 1.07903 ( 10) hydrogen bonds : bond 0.03711 ( 97) hydrogen bonds : angle 6.99558 ( 231) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.161 Fit side-chains REVERT: B 59 ASN cc_start: 0.5347 (m110) cc_final: 0.5127 (m110) REVERT: B 100 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6874 (m-80) REVERT: B 103 THR cc_start: 0.7526 (m) cc_final: 0.7152 (p) REVERT: B 148 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6570 (tpt90) REVERT: B 188 SER cc_start: 0.5459 (OUTLIER) cc_final: 0.4825 (t) REVERT: C 95 ASP cc_start: 0.6222 (OUTLIER) cc_final: 0.5977 (t0) REVERT: C 121 THR cc_start: 0.7792 (m) cc_final: 0.7445 (p) outliers start: 26 outliers final: 22 residues processed: 84 average time/residue: 0.0441 time to fit residues: 5.4319 Evaluate side-chains 91 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 210 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 15 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.192999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.174638 restraints weight = 6666.456| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 2.97 r_work: 0.4069 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4650 Z= 0.178 Angle : 0.696 9.618 6353 Z= 0.355 Chirality : 0.047 0.312 721 Planarity : 0.005 0.064 803 Dihedral : 5.681 42.935 639 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.01 % Favored : 87.65 % Rotamer: Outliers : 5.48 % Allowed : 33.46 % Favored : 61.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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 aren not related in a simple way. whole: -3.13 (0.33), residues: 591 helix: -0.25 (1.19), residues: 22 sheet: -2.12 (0.32), residues: 216 loop : -2.20 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 148 TYR 0.044 0.002 TYR B 100 PHE 0.008 0.001 PHE A 144 TRP 0.041 0.003 TRP A 103 HIS 0.012 0.002 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 4645) covalent geometry : angle 0.69521 ( 6343) SS BOND : bond 0.00441 ( 5) SS BOND : angle 1.01410 ( 10) hydrogen bonds : bond 0.03596 ( 97) hydrogen bonds : angle 6.96431 ( 231) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1301.22 seconds wall clock time: 23 minutes 8.75 seconds (1388.75 seconds total)