Starting phenix.real_space_refine on Fri Dec 27 15:32:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vad_31837/12_2024/7vad_31837.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vad_31837/12_2024/7vad_31837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vad_31837/12_2024/7vad_31837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vad_31837/12_2024/7vad_31837.map" model { file = "/net/cci-nas-00/data/ceres_data/7vad_31837/12_2024/7vad_31837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vad_31837/12_2024/7vad_31837.cif" } resolution = 3.41 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= 0.000 sd= 0.002 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 43 5.16 5 C 3676 2.51 5 N 912 2.21 5 O 1066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5697 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2344 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 17, 'TRANS': 288} Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1669 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 15, 'TRANS': 205} Chain: "L" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1684 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Time building chain proxies: 3.66, per 1000 atoms: 0.64 Number of scatterers: 5697 At special positions: 0 Unit cell: (87.15, 70.965, 143.175, 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 43 16.00 O 1066 8.00 N 912 7.00 C 3676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 785.6 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 11 sheets defined 37.4% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 21 through 44 Processing helix chain 'A' and resid 47 through 57 removed outlier: 3.870A pdb=" N ILE A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 70 Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 102 through 113 removed outlier: 4.080A pdb=" N ASN A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 142 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 156 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 211 removed outlier: 3.569A pdb=" N VAL A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 removed outlier: 3.856A pdb=" N MET A 218 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.550A pdb=" N ARG A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.588A pdb=" N PHE A 283 " --> pdb=" O GLY A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 284 through 308 removed outlier: 3.663A pdb=" N ILE A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.828A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.937A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 removed outlier: 3.621A pdb=" N LEU L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR L 131 " --> pdb=" O SER L 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.555A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.795A pdb=" N TYR H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 128 through 131 Processing sheet with id=AA5, first strand: chain 'H' and resid 143 through 146 removed outlier: 6.713A pdb=" N THR H 184 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA H 176 " --> pdb=" O THR H 184 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER H 186 " --> pdb=" O PHE H 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 159 through 161 removed outlier: 3.932A pdb=" N CYS H 203 " --> pdb=" O LYS H 216 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS H 216 " --> pdb=" O CYS H 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.848A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 40 through 43 removed outlier: 6.598A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 69 through 73 Processing sheet with id=AB1, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.854A pdb=" N ASN L 143 " --> pdb=" O TYR L 178 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 158 through 159 281 hydrogen bonds defined for protein. 762 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: 1.38 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1733 1.34 - 1.46: 1408 1.46 - 1.58: 2629 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 5835 Sorted by residual: bond pdb=" CB PRO H 126 " pdb=" CG PRO H 126 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.88e+00 bond pdb=" C LYS H 13 " pdb=" N PRO H 14 " ideal model delta sigma weight residual 1.337 1.346 -0.009 9.80e-03 1.04e+04 8.60e-01 bond pdb=" CB PRO A 276 " pdb=" CG PRO A 276 " ideal model delta sigma weight residual 1.492 1.536 -0.044 5.00e-02 4.00e+02 7.80e-01 bond pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.58e-01 bond pdb=" CG PRO H 126 " pdb=" CD PRO H 126 " ideal model delta sigma weight residual 1.503 1.530 -0.027 3.40e-02 8.65e+02 6.31e-01 ... (remaining 5830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 7753 1.57 - 3.15: 124 3.15 - 4.72: 33 4.72 - 6.30: 15 6.30 - 7.87: 4 Bond angle restraints: 7929 Sorted by residual: angle pdb=" C ALA H 16 " pdb=" CA ALA H 16 " pdb=" CB ALA H 16 " ideal model delta sigma weight residual 115.89 110.41 5.48 1.32e+00 5.74e-01 1.73e+01 angle pdb=" CA PRO H 126 " pdb=" N PRO H 126 " pdb=" CD PRO H 126 " ideal model delta sigma weight residual 112.00 106.55 5.45 1.40e+00 5.10e-01 1.52e+01 angle pdb=" N LEU A 150 " pdb=" CA LEU A 150 " pdb=" CB LEU A 150 " ideal model delta sigma weight residual 113.65 109.57 4.08 1.47e+00 4.63e-01 7.71e+00 angle pdb=" CB MET A 133 " pdb=" CG MET A 133 " pdb=" SD MET A 133 " ideal model delta sigma weight residual 112.70 120.57 -7.87 3.00e+00 1.11e-01 6.89e+00 angle pdb=" N GLY A 132 " pdb=" CA GLY A 132 " pdb=" C GLY A 132 " ideal model delta sigma weight residual 112.77 115.95 -3.18 1.28e+00 6.10e-01 6.19e+00 ... (remaining 7924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.79: 3022 13.79 - 27.58: 318 27.58 - 41.37: 116 41.37 - 55.16: 23 55.16 - 68.95: 2 Dihedral angle restraints: 3481 sinusoidal: 1329 harmonic: 2152 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 94 " pdb=" CB CYS L 94 " ideal model delta sinusoidal sigma weight residual 93.00 161.95 -68.95 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 65.54 27.46 1 1.00e+01 1.00e-02 1.08e+01 dihedral pdb=" CA GLU A 277 " pdb=" CB GLU A 277 " pdb=" CG GLU A 277 " pdb=" CD GLU A 277 " ideal model delta sinusoidal sigma weight residual -60.00 -114.46 54.46 3 1.50e+01 4.44e-03 9.28e+00 ... (remaining 3478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 555 0.029 - 0.059: 241 0.059 - 0.088: 71 0.088 - 0.117: 45 0.117 - 0.147: 6 Chirality restraints: 918 Sorted by residual: chirality pdb=" CA ILE H 104 " pdb=" N ILE H 104 " pdb=" C ILE H 104 " pdb=" CB ILE H 104 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA MET A 133 " pdb=" N MET A 133 " pdb=" C MET A 133 " pdb=" CB MET A 133 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CB VAL L 19 " pdb=" CA VAL L 19 " pdb=" CG1 VAL L 19 " pdb=" CG2 VAL L 19 " both_signs ideal model delta sigma weight residual False -2.63 -2.76 0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 915 not shown) Planarity restraints: 980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 125 " 0.086 5.00e-02 4.00e+02 1.29e-01 2.64e+01 pdb=" N PRO H 126 " -0.222 5.00e-02 4.00e+02 pdb=" CA PRO H 126 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO H 126 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 275 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 276 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 290 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C MET A 290 " -0.024 2.00e-02 2.50e+03 pdb=" O MET A 290 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE A 291 " 0.008 2.00e-02 2.50e+03 ... (remaining 977 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 856 2.76 - 3.30: 5560 3.30 - 3.83: 9163 3.83 - 4.37: 10150 4.37 - 4.90: 17934 Nonbonded interactions: 43663 Sorted by model distance: nonbonded pdb=" OE1 GLN L 6 " pdb=" OG1 THR L 107 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR L 69 " pdb=" OG1 THR L 80 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A 105 " pdb=" OE1 GLU A 257 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR H 28 " pdb=" OG SER H 31 " model vdw 2.287 3.040 nonbonded pdb=" OD1 ASP H 102 " pdb=" N GLY H 103 " model vdw 2.302 3.120 ... (remaining 43658 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: 0.500 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 16.400 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 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 : 0.002 0.085 5835 Z= 0.147 Angle : 0.592 7.872 7929 Z= 0.294 Chirality : 0.040 0.147 918 Planarity : 0.006 0.129 980 Dihedral : 13.009 60.281 2096 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.31), residues: 737 helix: 1.37 (0.33), residues: 236 sheet: 0.80 (0.41), residues: 168 loop : -0.92 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 111 HIS 0.004 0.001 HIS L 194 PHE 0.017 0.001 PHE A 244 TYR 0.007 0.001 TYR A 69 ARG 0.007 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8328 (tp) cc_final: 0.8022 (tp) REVERT: A 153 LYS cc_start: 0.8373 (mttm) cc_final: 0.8132 (ttmm) REVERT: A 251 ARG cc_start: 0.7777 (ptp90) cc_final: 0.7564 (ptp90) REVERT: L 162 ASN cc_start: 0.7902 (t0) cc_final: 0.7676 (m-40) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.1462 time to fit residues: 55.2889 Evaluate side-chains 235 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 209 ASN H 172 HIS L 37 ASN L 44 GLN L 129 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5835 Z= 0.311 Angle : 0.715 10.390 7929 Z= 0.353 Chirality : 0.045 0.159 918 Planarity : 0.006 0.080 980 Dihedral : 4.101 16.419 794 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.49 % Allowed : 18.89 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.31), residues: 737 helix: 1.72 (0.33), residues: 251 sheet: 0.75 (0.40), residues: 180 loop : -1.10 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 56 HIS 0.005 0.001 HIS L 194 PHE 0.016 0.002 PHE A 231 TYR 0.020 0.002 TYR A 289 ARG 0.006 0.001 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 250 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 251 ARG cc_start: 0.7743 (ptp90) cc_final: 0.7494 (ptp90) REVERT: H 100 TYR cc_start: 0.8548 (t80) cc_final: 0.8269 (t80) REVERT: H 151 LYS cc_start: 0.7808 (mmtp) cc_final: 0.7580 (mmtp) REVERT: L 44 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8466 (tt0) REVERT: L 95 LYS cc_start: 0.9237 (ttpt) cc_final: 0.9017 (ttpt) outliers start: 29 outliers final: 19 residues processed: 261 average time/residue: 0.1479 time to fit residues: 51.6022 Evaluate side-chains 255 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 235 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain L residue 44 GLN Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 137 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 0.0060 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 0.0030 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.7608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 87 ASN A 106 ASN A 209 ASN A 247 ASN L 44 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5835 Z= 0.202 Angle : 0.664 10.357 7929 Z= 0.321 Chirality : 0.043 0.154 918 Planarity : 0.005 0.064 980 Dihedral : 4.099 16.714 794 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.80 % Allowed : 24.15 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.31), residues: 737 helix: 1.82 (0.33), residues: 246 sheet: 0.77 (0.40), residues: 180 loop : -1.17 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 305 HIS 0.009 0.002 HIS L 194 PHE 0.022 0.002 PHE A 108 TYR 0.014 0.001 TYR A 289 ARG 0.013 0.001 ARG L 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 243 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 241 SER cc_start: 0.8429 (p) cc_final: 0.8087 (p) REVERT: L 44 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8471 (tt0) outliers start: 31 outliers final: 22 residues processed: 256 average time/residue: 0.1334 time to fit residues: 47.1066 Evaluate side-chains 254 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 231 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 44 GLN Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 87 ASN A 106 ASN A 209 ASN A 247 ASN H 172 HIS L 44 GLN L 129 GLN L 194 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5835 Z= 0.279 Angle : 0.689 8.890 7929 Z= 0.338 Chirality : 0.044 0.149 918 Planarity : 0.005 0.056 980 Dihedral : 4.274 17.840 794 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 7.89 % Allowed : 23.84 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.31), residues: 737 helix: 1.90 (0.33), residues: 241 sheet: 0.62 (0.39), residues: 186 loop : -1.16 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 305 HIS 0.003 0.001 HIS H 172 PHE 0.018 0.002 PHE H 154 TYR 0.018 0.002 TYR H 54 ARG 0.007 0.001 ARG L 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 264 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 209 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7910 (m-40) REVERT: A 241 SER cc_start: 0.8588 (p) cc_final: 0.8382 (p) REVERT: A 249 ARG cc_start: 0.8346 (ttt-90) cc_final: 0.8123 (ttt-90) REVERT: H 62 GLU cc_start: 0.7074 (pp20) cc_final: 0.6798 (pp20) REVERT: H 89 GLU cc_start: 0.8397 (pp20) cc_final: 0.7941 (pp20) REVERT: H 159 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8923 (p) outliers start: 51 outliers final: 37 residues processed: 283 average time/residue: 0.1386 time to fit residues: 53.4314 Evaluate side-chains 295 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 256 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 chunk 52 optimal weight: 0.0070 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 87 ASN A 106 ASN A 247 ASN H 39 GLN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN L 194 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5835 Z= 0.189 Angle : 0.681 8.956 7929 Z= 0.330 Chirality : 0.043 0.160 918 Planarity : 0.004 0.052 980 Dihedral : 4.208 17.760 794 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 5.57 % Allowed : 27.55 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.31), residues: 737 helix: 1.84 (0.33), residues: 250 sheet: 0.63 (0.40), residues: 180 loop : -1.17 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 153 HIS 0.003 0.001 HIS H 35 PHE 0.019 0.001 PHE A 108 TYR 0.018 0.001 TYR L 98 ARG 0.007 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 256 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 209 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7865 (m-40) REVERT: A 241 SER cc_start: 0.8526 (p) cc_final: 0.8295 (p) REVERT: H 62 GLU cc_start: 0.6985 (pp20) cc_final: 0.6738 (pp20) REVERT: H 159 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8903 (p) REVERT: L 123 PHE cc_start: 0.8859 (m-80) cc_final: 0.8551 (m-80) REVERT: L 153 TRP cc_start: 0.7841 (m100) cc_final: 0.7539 (m100) outliers start: 36 outliers final: 24 residues processed: 269 average time/residue: 0.1330 time to fit residues: 48.9425 Evaluate side-chains 273 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 247 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 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 87 ASN A 106 ASN A 247 ASN L 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5835 Z= 0.216 Angle : 0.700 8.770 7929 Z= 0.341 Chirality : 0.043 0.148 918 Planarity : 0.004 0.051 980 Dihedral : 4.243 17.282 794 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 6.50 % Allowed : 27.86 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.31), residues: 737 helix: 1.94 (0.33), residues: 244 sheet: 0.60 (0.40), residues: 180 loop : -1.14 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 153 HIS 0.003 0.001 HIS L 194 PHE 0.017 0.001 PHE A 108 TYR 0.018 0.002 TYR L 98 ARG 0.007 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 250 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 209 ASN cc_start: 0.8181 (m-40) cc_final: 0.7840 (m110) REVERT: A 251 ARG cc_start: 0.8019 (ptp90) cc_final: 0.7607 (ptp90) REVERT: H 62 GLU cc_start: 0.7016 (pp20) cc_final: 0.6794 (pp20) REVERT: H 159 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8958 (p) REVERT: L 123 PHE cc_start: 0.8898 (m-80) cc_final: 0.8456 (m-80) outliers start: 42 outliers final: 36 residues processed: 263 average time/residue: 0.1309 time to fit residues: 46.9916 Evaluate side-chains 282 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 245 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 87 ASN A 106 ASN A 247 ASN L 194 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5835 Z= 0.238 Angle : 0.710 8.756 7929 Z= 0.349 Chirality : 0.044 0.147 918 Planarity : 0.004 0.050 980 Dihedral : 4.316 17.468 794 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 7.74 % Allowed : 27.86 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.31), residues: 737 helix: 1.96 (0.33), residues: 243 sheet: 0.50 (0.40), residues: 180 loop : -1.23 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP L 153 HIS 0.003 0.001 HIS L 194 PHE 0.017 0.001 PHE A 108 TYR 0.020 0.002 TYR L 98 ARG 0.009 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 242 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 209 ASN cc_start: 0.8193 (m-40) cc_final: 0.7759 (m110) REVERT: H 62 GLU cc_start: 0.7068 (pp20) cc_final: 0.6860 (pp20) REVERT: H 89 GLU cc_start: 0.8379 (pp20) cc_final: 0.7941 (pp20) REVERT: H 159 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8893 (p) REVERT: L 123 PHE cc_start: 0.8880 (m-80) cc_final: 0.8458 (m-80) outliers start: 50 outliers final: 41 residues processed: 262 average time/residue: 0.1428 time to fit residues: 50.8679 Evaluate side-chains 282 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 240 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 5.9990 chunk 21 optimal weight: 0.0570 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 87 ASN A 106 ASN L 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5835 Z= 0.202 Angle : 0.707 8.763 7929 Z= 0.341 Chirality : 0.044 0.163 918 Planarity : 0.004 0.049 980 Dihedral : 4.318 17.252 794 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 6.81 % Allowed : 28.79 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.31), residues: 737 helix: 1.93 (0.33), residues: 243 sheet: 0.52 (0.40), residues: 175 loop : -1.21 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP L 153 HIS 0.003 0.001 HIS L 194 PHE 0.016 0.001 PHE A 108 TYR 0.020 0.002 TYR L 98 ARG 0.008 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 0.717 Fit side-chains REVERT: A 133 MET cc_start: 0.7260 (ppp) cc_final: 0.6909 (ppp) REVERT: A 209 ASN cc_start: 0.8178 (m-40) cc_final: 0.7755 (m110) REVERT: A 249 ARG cc_start: 0.8198 (ttt-90) cc_final: 0.7797 (tpt-90) REVERT: H 89 GLU cc_start: 0.8372 (pp20) cc_final: 0.7908 (pp20) REVERT: H 159 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8899 (p) REVERT: L 123 PHE cc_start: 0.8868 (m-80) cc_final: 0.8410 (m-80) outliers start: 44 outliers final: 38 residues processed: 257 average time/residue: 0.1327 time to fit residues: 47.0412 Evaluate side-chains 277 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 238 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 0.0970 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 106 ASN A 247 ASN L 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5835 Z= 0.250 Angle : 0.734 8.794 7929 Z= 0.357 Chirality : 0.045 0.188 918 Planarity : 0.004 0.048 980 Dihedral : 4.400 17.388 794 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 7.43 % Allowed : 28.33 % Favored : 64.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.31), residues: 737 helix: 2.01 (0.33), residues: 240 sheet: 0.41 (0.40), residues: 176 loop : -1.29 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP L 153 HIS 0.003 0.001 HIS L 194 PHE 0.016 0.001 PHE A 108 TYR 0.021 0.002 TYR L 98 ARG 0.009 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 246 time to evaluate : 0.673 Fit side-chains REVERT: A 133 MET cc_start: 0.7443 (ppp) cc_final: 0.7149 (ppp) REVERT: A 209 ASN cc_start: 0.8219 (m-40) cc_final: 0.7789 (m110) REVERT: H 89 GLU cc_start: 0.8385 (pp20) cc_final: 0.7946 (pp20) REVERT: H 159 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8929 (p) REVERT: L 123 PHE cc_start: 0.8891 (m-80) cc_final: 0.8438 (m-80) REVERT: L 210 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8556 (tp) outliers start: 48 outliers final: 42 residues processed: 265 average time/residue: 0.1395 time to fit residues: 50.3911 Evaluate side-chains 284 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 210 ILE Chi-restraints excluded: chain L residue 211 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 106 ASN A 247 ASN L 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5835 Z= 0.230 Angle : 0.749 8.946 7929 Z= 0.365 Chirality : 0.045 0.199 918 Planarity : 0.005 0.079 980 Dihedral : 4.425 17.457 794 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 7.59 % Allowed : 28.64 % Favored : 63.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.31), residues: 737 helix: 1.95 (0.33), residues: 240 sheet: 0.40 (0.42), residues: 166 loop : -1.26 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP L 153 HIS 0.003 0.001 HIS L 194 PHE 0.016 0.001 PHE A 108 TYR 0.021 0.002 TYR L 98 ARG 0.011 0.001 ARG A 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 242 time to evaluate : 0.686 Fit side-chains REVERT: A 133 MET cc_start: 0.7431 (ppp) cc_final: 0.7133 (ppp) REVERT: A 209 ASN cc_start: 0.8289 (m-40) cc_final: 0.7891 (m110) REVERT: H 89 GLU cc_start: 0.8373 (pp20) cc_final: 0.7934 (pp20) REVERT: H 159 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8924 (p) REVERT: L 123 PHE cc_start: 0.8885 (m-80) cc_final: 0.8435 (m-80) REVERT: L 210 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8563 (tp) outliers start: 49 outliers final: 42 residues processed: 261 average time/residue: 0.1328 time to fit residues: 47.2899 Evaluate side-chains 284 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 210 ILE Chi-restraints excluded: chain L residue 211 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.137146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.110754 restraints weight = 10768.502| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.49 r_work: 0.3231 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5835 Z= 0.233 Angle : 0.747 8.887 7929 Z= 0.366 Chirality : 0.045 0.196 918 Planarity : 0.005 0.051 980 Dihedral : 4.463 18.269 794 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 6.81 % Allowed : 29.57 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.31), residues: 737 helix: 1.95 (0.33), residues: 240 sheet: 0.37 (0.42), residues: 166 loop : -1.28 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP L 153 HIS 0.003 0.001 HIS L 194 PHE 0.017 0.001 PHE A 108 TYR 0.021 0.002 TYR L 98 ARG 0.009 0.001 ARG A 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1697.69 seconds wall clock time: 31 minutes 47.31 seconds (1907.31 seconds total)