Starting phenix.real_space_refine on Wed Jul 23 22:34:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ccs_45456/07_2025/9ccs_45456.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ccs_45456/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ccs_45456/07_2025/9ccs_45456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ccs_45456/07_2025/9ccs_45456.map" model { file = "/net/cci-nas-00/data/ceres_data/9ccs_45456/07_2025/9ccs_45456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ccs_45456/07_2025/9ccs_45456.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.43, per 1000 atoms: 0.76 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: 1.00 Conformation dependent library (CDL) restraints added in 535.6 milliseconds 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: 1.14 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: 1.49 Time building geometry restraints manager: 1.22 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.940 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.530 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.057 0.004 TRP B 102 HIS 0.009 0.002 HIS C 40 PHE 0.014 0.003 PHE A 144 TYR 0.050 0.003 TYR B 100 ARG 0.002 0.000 ARG C 45 Details of bonding type rmsd hydrogen bonds : bond 0.18540 ( 97) hydrogen bonds : angle 9.10184 ( 231) SS BOND : bond 0.00792 ( 5) SS BOND : angle 1.57221 ( 10) covalent geometry : bond 0.00616 ( 4645) covalent geometry : angle 0.86621 ( 6343) *********************** 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 : 0.440 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 76 average time/residue: 0.1178 time to fit residues: 12.4812 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 : 0.491 ------------------------------------------------------------------------------- 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 48 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 15 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4426 r_free = 0.4426 target = 0.191893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.173713 restraints weight = 6554.393| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 2.91 r_work: 0.4075 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4650 Z= 0.182 Angle : 0.668 7.563 6353 Z= 0.351 Chirality : 0.045 0.153 721 Planarity : 0.006 0.075 803 Dihedral : 6.306 46.212 644 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.17 % Favored : 88.49 % Rotamer: Outliers : 4.31 % Allowed : 32.29 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.32), residues: 591 helix: -1.47 (0.90), residues: 21 sheet: -2.19 (0.31), residues: 207 loop : -2.18 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 102 HIS 0.006 0.001 HIS C 40 PHE 0.010 0.002 PHE A 142 TYR 0.017 0.002 TYR B 100 ARG 0.004 0.001 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 97) hydrogen bonds : angle 7.94832 ( 231) SS BOND : bond 0.00536 ( 5) SS BOND : angle 1.09953 ( 10) covalent geometry : bond 0.00395 ( 4645) covalent geometry : angle 0.66749 ( 6343) *********************** 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 99 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.442 Fit side-chains REVERT: C 121 THR cc_start: 0.7629 (m) cc_final: 0.7391 (p) outliers start: 22 outliers final: 9 residues processed: 91 average time/residue: 0.1095 time to fit residues: 14.0143 Evaluate side-chains 85 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 181 LEU Chi-restraints excluded: chain C residue 9 LEU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 0.2980 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4378 r_free = 0.4378 target = 0.185592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.167423 restraints weight = 6639.069| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 2.86 r_work: 0.4055 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 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 : 0.004 0.044 4650 Z= 0.207 Angle : 0.683 9.624 6353 Z= 0.353 Chirality : 0.046 0.237 721 Planarity : 0.006 0.077 803 Dihedral : 5.885 43.234 639 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.84 % Favored : 87.82 % Rotamer: Outliers : 6.07 % Allowed : 30.53 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.33), residues: 591 helix: -0.95 (1.02), residues: 22 sheet: -2.14 (0.31), residues: 212 loop : -2.14 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 97 HIS 0.009 0.002 HIS C 40 PHE 0.009 0.002 PHE C 113 TYR 0.011 0.002 TYR B 77 ARG 0.003 0.000 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 97) hydrogen bonds : angle 7.64808 ( 231) SS BOND : bond 0.00529 ( 5) SS BOND : angle 1.19262 ( 10) covalent geometry : bond 0.00445 ( 4645) covalent geometry : angle 0.68159 ( 6343) *********************** 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: 31 poor density : 72 time to evaluate : 0.652 Fit side-chains REVERT: C 121 THR cc_start: 0.7683 (m) cc_final: 0.7416 (p) outliers start: 31 outliers final: 18 residues processed: 93 average time/residue: 0.1270 time to fit residues: 16.9738 Evaluate side-chains 90 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 32 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 115 THR 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 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 190 SER Chi-restraints excluded: chain C residue 210 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 39 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 8 optimal weight: 0.0970 chunk 10 optimal weight: 0.0870 chunk 30 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.4756 ------------------------------------------------------------------------------- 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 59 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.188423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.170570 restraints weight = 6638.540| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.86 r_work: 0.4089 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4650 Z= 0.158 Angle : 0.645 8.723 6353 Z= 0.335 Chirality : 0.046 0.246 721 Planarity : 0.006 0.075 803 Dihedral : 5.701 41.165 639 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.00 % Favored : 88.66 % Rotamer: Outliers : 5.28 % Allowed : 31.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.33), residues: 591 helix: -0.50 (1.07), residues: 22 sheet: -2.02 (0.32), residues: 205 loop : -2.19 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 97 HIS 0.009 0.002 HIS C 40 PHE 0.009 0.001 PHE A 144 TYR 0.009 0.001 TYR B 55 ARG 0.003 0.000 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 97) hydrogen bonds : angle 7.35976 ( 231) SS BOND : bond 0.00402 ( 5) SS BOND : angle 1.00029 ( 10) covalent geometry : bond 0.00345 ( 4645) covalent geometry : angle 0.64456 ( 6343) *********************** 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 98 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: C 121 THR cc_start: 0.7704 (m) cc_final: 0.7426 (p) outliers start: 27 outliers final: 17 residues processed: 89 average time/residue: 0.1158 time to fit residues: 14.7748 Evaluate side-chains 86 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 170 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 0 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 47 optimal weight: 0.0970 chunk 23 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 59 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.192619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.174461 restraints weight = 6716.554| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 2.97 r_work: 0.4074 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.1514 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= 0.167 Angle : 0.648 6.334 6353 Z= 0.337 Chirality : 0.046 0.254 721 Planarity : 0.005 0.072 803 Dihedral : 5.719 43.009 639 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.34 % Favored : 88.32 % Rotamer: Outliers : 5.28 % Allowed : 31.51 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.33), residues: 591 helix: -0.22 (1.13), residues: 21 sheet: -2.01 (0.32), residues: 208 loop : -2.15 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 41 HIS 0.008 0.002 HIS C 40 PHE 0.008 0.001 PHE A 144 TYR 0.035 0.002 TYR B 100 ARG 0.002 0.000 ARG C 45 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 97) hydrogen bonds : angle 7.29812 ( 231) SS BOND : bond 0.00431 ( 5) SS BOND : angle 0.94359 ( 10) covalent geometry : bond 0.00365 ( 4645) covalent geometry : angle 0.64790 ( 6343) *********************** 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: 27 poor density : 75 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: C 121 THR cc_start: 0.7734 (m) cc_final: 0.7433 (p) outliers start: 27 outliers final: 19 residues processed: 90 average time/residue: 0.1101 time to fit residues: 14.0194 Evaluate side-chains 94 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 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 170 THR 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 76 THR 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 56 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 59 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.185890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.167821 restraints weight = 6648.322| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 2.84 r_work: 0.4048 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4650 Z= 0.216 Angle : 0.682 8.516 6353 Z= 0.353 Chirality : 0.047 0.278 721 Planarity : 0.006 0.069 803 Dihedral : 5.840 44.070 639 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.68 % Favored : 87.99 % Rotamer: Outliers : 5.87 % Allowed : 31.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.33), residues: 591 helix: -0.14 (1.15), residues: 21 sheet: -2.17 (0.31), residues: 226 loop : -2.16 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 41 HIS 0.010 0.002 HIS C 40 PHE 0.008 0.002 PHE C 135 TYR 0.047 0.002 TYR B 100 ARG 0.002 0.000 ARG C 45 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 97) hydrogen bonds : angle 7.33822 ( 231) SS BOND : bond 0.00524 ( 5) SS BOND : angle 1.03155 ( 10) covalent geometry : bond 0.00470 ( 4645) covalent geometry : angle 0.68153 ( 6343) *********************** 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 101 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: C 15 GLU cc_start: 0.5880 (OUTLIER) cc_final: 0.5422 (pt0) REVERT: C 95 ASP cc_start: 0.5973 (OUTLIER) cc_final: 0.5754 (t0) outliers start: 30 outliers final: 21 residues processed: 90 average time/residue: 0.1073 time to fit residues: 13.9256 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 : 0.499 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 45 optimal weight: 0.0970 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 59 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.187397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.169594 restraints weight = 6580.556| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.84 r_work: 0.4065 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4650 Z= 0.181 Angle : 0.668 9.767 6353 Z= 0.346 Chirality : 0.047 0.284 721 Planarity : 0.005 0.066 803 Dihedral : 5.790 43.421 639 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.68 % Favored : 87.99 % Rotamer: Outliers : 5.87 % Allowed : 31.90 % Favored : 62.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.33), residues: 591 helix: 0.03 (1.19), residues: 21 sheet: -2.12 (0.31), residues: 226 loop : -2.15 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 41 HIS 0.009 0.002 HIS C 40 PHE 0.008 0.001 PHE A 144 TYR 0.044 0.002 TYR B 100 ARG 0.002 0.000 ARG C 45 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 97) hydrogen bonds : angle 7.16628 ( 231) SS BOND : bond 0.00466 ( 5) SS BOND : angle 0.98033 ( 10) covalent geometry : bond 0.00399 ( 4645) covalent geometry : angle 0.66745 ( 6343) *********************** 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 97 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: C 15 GLU cc_start: 0.5846 (OUTLIER) cc_final: 0.5394 (pt0) REVERT: C 95 ASP cc_start: 0.5959 (OUTLIER) cc_final: 0.5705 (t0) outliers start: 30 outliers final: 21 residues processed: 87 average time/residue: 0.1052 time to fit residues: 13.1344 Evaluate side-chains 88 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 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 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 209 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 0.0970 chunk 5 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 59 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.186717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.168557 restraints weight = 6600.814| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.84 r_work: 0.4059 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4650 Z= 0.197 Angle : 0.685 9.980 6353 Z= 0.354 Chirality : 0.047 0.301 721 Planarity : 0.005 0.064 803 Dihedral : 5.811 43.414 639 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.18 % Favored : 87.48 % Rotamer: Outliers : 5.28 % Allowed : 33.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.33), residues: 591 helix: 0.08 (1.18), residues: 21 sheet: -2.12 (0.31), residues: 226 loop : -2.23 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 41 HIS 0.010 0.002 HIS C 40 PHE 0.009 0.001 PHE A 144 TYR 0.040 0.002 TYR B 100 ARG 0.002 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 97) hydrogen bonds : angle 7.13590 ( 231) SS BOND : bond 0.00517 ( 5) SS BOND : angle 1.03041 ( 10) covalent geometry : bond 0.00433 ( 4645) covalent geometry : angle 0.68445 ( 6343) *********************** 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 91 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: B 172 GLN cc_start: 0.7070 (OUTLIER) cc_final: 0.6844 (mm-40) REVERT: C 15 GLU cc_start: 0.5859 (OUTLIER) cc_final: 0.5406 (pt0) REVERT: C 95 ASP cc_start: 0.6028 (OUTLIER) cc_final: 0.5733 (t0) REVERT: C 161 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7073 (mm-30) outliers start: 27 outliers final: 21 residues processed: 83 average time/residue: 0.1096 time to fit residues: 13.0969 Evaluate side-chains 87 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 170 THR Chi-restraints excluded: chain B residue 172 GLN 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 95 ASP Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 209 CYS 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 22 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 42 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 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 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.191281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.172964 restraints weight = 6608.963| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 2.93 r_work: 0.4056 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4650 Z= 0.190 Angle : 0.687 7.326 6353 Z= 0.355 Chirality : 0.047 0.304 721 Planarity : 0.005 0.065 803 Dihedral : 5.775 43.664 639 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.68 % Favored : 87.99 % Rotamer: Outliers : 5.87 % Allowed : 32.29 % Favored : 61.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.33), residues: 591 helix: 0.12 (1.19), residues: 21 sheet: -2.07 (0.31), residues: 230 loop : -2.19 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 103 HIS 0.011 0.002 HIS C 40 PHE 0.009 0.002 PHE C 135 TYR 0.048 0.002 TYR B 100 ARG 0.002 0.000 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 97) hydrogen bonds : angle 7.07278 ( 231) SS BOND : bond 0.00587 ( 5) SS BOND : angle 1.22237 ( 10) covalent geometry : bond 0.00424 ( 4645) covalent geometry : angle 0.68584 ( 6343) *********************** 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 95 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: B 172 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6858 (mm-40) REVERT: C 15 GLU cc_start: 0.5804 (OUTLIER) cc_final: 0.5377 (pt0) REVERT: C 95 ASP cc_start: 0.6087 (OUTLIER) cc_final: 0.5778 (t0) REVERT: C 121 THR cc_start: 0.7782 (m) cc_final: 0.7441 (p) REVERT: C 161 GLU cc_start: 0.7265 (mm-30) cc_final: 0.7013 (mm-30) outliers start: 30 outliers final: 22 residues processed: 85 average time/residue: 0.1070 time to fit residues: 13.1164 Evaluate side-chains 90 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 25 THR 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 170 THR Chi-restraints excluded: chain B residue 172 GLN 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 95 ASP Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 209 CYS 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 3 optimal weight: 0.0570 chunk 56 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 0.0970 chunk 53 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 59 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.193843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.175614 restraints weight = 6624.010| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 2.94 r_work: 0.4109 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4650 Z= 0.151 Angle : 0.668 6.598 6353 Z= 0.346 Chirality : 0.047 0.309 721 Planarity : 0.006 0.065 803 Dihedral : 5.647 42.635 639 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.51 % Favored : 88.16 % Rotamer: Outliers : 4.89 % Allowed : 33.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.33), residues: 591 helix: 0.19 (1.24), residues: 21 sheet: -2.03 (0.32), residues: 223 loop : -2.19 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 103 HIS 0.010 0.002 HIS C 40 PHE 0.010 0.002 PHE A 144 TYR 0.044 0.002 TYR B 100 ARG 0.002 0.000 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 97) hydrogen bonds : angle 6.88903 ( 231) SS BOND : bond 0.00437 ( 5) SS BOND : angle 0.95042 ( 10) covalent geometry : bond 0.00342 ( 4645) covalent geometry : angle 0.66749 ( 6343) ********************** 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 91 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 95 TYR cc_start: 0.7036 (m-10) cc_final: 0.6634 (m-10) REVERT: C 95 ASP cc_start: 0.6032 (OUTLIER) cc_final: 0.5750 (t0) REVERT: C 161 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6920 (mm-30) outliers start: 25 outliers final: 22 residues processed: 83 average time/residue: 0.1127 time to fit residues: 13.3652 Evaluate side-chains 87 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 25 THR 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 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 34 PHE Chi-restraints excluded: chain C residue 86 MET 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 159 PHE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 209 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 1 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 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 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.192394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.173712 restraints weight = 6604.843| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 2.96 r_work: 0.4060 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4650 Z= 0.190 Angle : 0.702 6.811 6353 Z= 0.363 Chirality : 0.048 0.318 721 Planarity : 0.006 0.065 803 Dihedral : 5.675 43.234 639 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.68 % Favored : 87.99 % Rotamer: Outliers : 5.28 % Allowed : 32.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.34), residues: 591 helix: 0.19 (1.23), residues: 21 sheet: -2.10 (0.31), residues: 230 loop : -2.13 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 103 HIS 0.013 0.002 HIS C 40 PHE 0.009 0.001 PHE C 135 TYR 0.051 0.002 TYR B 100 ARG 0.003 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 97) hydrogen bonds : angle 6.96578 ( 231) SS BOND : bond 0.00511 ( 5) SS BOND : angle 1.07663 ( 10) covalent geometry : bond 0.00428 ( 4645) covalent geometry : angle 0.70080 ( 6343) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2502.43 seconds wall clock time: 44 minutes 3.83 seconds (2643.83 seconds total)