Starting phenix.real_space_refine on Sun Dec 29 23:27:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qsr_18640/12_2024/8qsr_18640.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qsr_18640/12_2024/8qsr_18640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qsr_18640/12_2024/8qsr_18640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qsr_18640/12_2024/8qsr_18640.map" model { file = "/net/cci-nas-00/data/ceres_data/8qsr_18640/12_2024/8qsr_18640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qsr_18640/12_2024/8qsr_18640.cif" } resolution = 2.56 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 28 5.16 5 C 3870 2.51 5 N 932 2.21 5 O 978 1.98 5 H 5938 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 11746 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 5861 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 22, 'TRANS': 360} Chain: "B" Number of atoms: 5861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 5861 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 22, 'TRANS': 360} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'BGC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'BGC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.66, per 1000 atoms: 0.48 Number of scatterers: 11746 At special positions: 0 Unit cell: (113.197, 76.4325, 71.595, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 O 978 8.00 N 932 7.00 C 3870 6.00 H 5938 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.3 seconds 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 2 sheets defined 84.7% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 4 through 22 Proline residue: A 19 - end of helix removed outlier: 3.813A pdb=" N VAL A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 36 removed outlier: 4.033A pdb=" N ALA A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN A 36 " --> pdb=" O VAL A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 58 removed outlier: 3.629A pdb=" N ASN A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 71 Processing helix chain 'A' and resid 75 through 102 Proline residue: A 98 - end of helix Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 117 through 136 Processing helix chain 'A' and resid 141 through 145 removed outlier: 3.573A pdb=" N GLY A 145 " --> pdb=" O GLU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 151 removed outlier: 3.912A pdb=" N ARG A 151 " --> pdb=" O ALA A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 151' Processing helix chain 'A' and resid 152 through 189 Proline residue: A 173 - end of helix Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 210 through 221 Proline residue: A 217 - end of helix Processing helix chain 'A' and resid 235 through 243 Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 251 through 258 removed outlier: 4.179A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 272 Processing helix chain 'A' and resid 273 through 276 Processing helix chain 'A' and resid 277 through 294 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 308 through 330 removed outlier: 3.671A pdb=" N PHE A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 340 through 347 Processing helix chain 'A' and resid 348 through 351 Processing helix chain 'A' and resid 355 through 380 removed outlier: 3.916A pdb=" N ILE A 359 " --> pdb=" O TRP A 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 22 Proline residue: B 19 - end of helix removed outlier: 3.812A pdb=" N VAL B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 removed outlier: 4.033A pdb=" N ALA B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN B 36 " --> pdb=" O VAL B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 58 removed outlier: 3.628A pdb=" N ASN B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 71 Processing helix chain 'B' and resid 75 through 102 removed outlier: 3.503A pdb=" N ALA B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 117 through 136 Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.573A pdb=" N GLY B 145 " --> pdb=" O GLU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 151 removed outlier: 3.920A pdb=" N ARG B 151 " --> pdb=" O ALA B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 151' Processing helix chain 'B' and resid 152 through 189 Proline residue: B 173 - end of helix Processing helix chain 'B' and resid 190 through 206 Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 210 through 221 Proline residue: B 217 - end of helix Processing helix chain 'B' and resid 235 through 243 Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 251 through 258 removed outlier: 4.180A pdb=" N LEU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 273 through 276 Processing helix chain 'B' and resid 277 through 294 Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 308 through 330 removed outlier: 3.671A pdb=" N PHE B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 340 through 347 Processing helix chain 'B' and resid 348 through 351 Processing helix chain 'B' and resid 355 through 380 removed outlier: 3.917A pdb=" N ILE B 359 " --> pdb=" O TRP B 355 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 226 Processing sheet with id=AA2, first strand: chain 'B' and resid 225 through 226 422 hydrogen bonds defined for protein. 1242 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: 4.53 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5934 1.03 - 1.22: 14 1.22 - 1.42: 2499 1.42 - 1.61: 3415 1.61 - 1.81: 52 Bond restraints: 11914 Sorted by residual: bond pdb=" NE ARG A 151 " pdb=" HE ARG A 151 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" NE ARG B 151 " pdb=" HE ARG B 151 " ideal model delta sigma weight residual 0.860 0.969 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C GLU A 202 " pdb=" O GLU A 202 " ideal model delta sigma weight residual 1.236 1.181 0.056 1.15e-02 7.56e+03 2.33e+01 bond pdb=" C GLU A 298 " pdb=" O GLU A 298 " ideal model delta sigma weight residual 1.238 1.188 0.050 1.28e-02 6.10e+03 1.53e+01 bond pdb=" NZ LYS B 91 " pdb=" HZ3 LYS B 91 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.24e+01 ... (remaining 11909 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 18603 1.25 - 2.50: 1740 2.50 - 3.74: 1130 3.74 - 4.99: 88 4.99 - 6.24: 51 Bond angle restraints: 21612 Sorted by residual: angle pdb=" CA ASP A 75 " pdb=" C ASP A 75 " pdb=" N GLY A 76 " ideal model delta sigma weight residual 116.28 119.99 -3.71 1.26e+00 6.30e-01 8.66e+00 angle pdb=" C ASP B 75 " pdb=" N GLY B 76 " pdb=" CA GLY B 76 " ideal model delta sigma weight residual 120.22 123.90 -3.68 1.27e+00 6.20e-01 8.41e+00 angle pdb=" CA ASP B 75 " pdb=" C ASP B 75 " pdb=" N GLY B 76 " ideal model delta sigma weight residual 116.28 119.82 -3.54 1.26e+00 6.30e-01 7.88e+00 angle pdb=" C ASP A 75 " pdb=" N GLY A 76 " pdb=" CA GLY A 76 " ideal model delta sigma weight residual 120.22 123.67 -3.45 1.27e+00 6.20e-01 7.40e+00 angle pdb=" C GLU A 202 " pdb=" CA GLU A 202 " pdb=" CB GLU A 202 " ideal model delta sigma weight residual 110.88 106.81 4.07 1.57e+00 4.06e-01 6.72e+00 ... (remaining 21607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 5192 15.76 - 31.52: 252 31.52 - 47.28: 97 47.28 - 63.04: 124 63.04 - 78.80: 3 Dihedral angle restraints: 5668 sinusoidal: 2990 harmonic: 2678 Sorted by residual: dihedral pdb=" CA ILE A 171 " pdb=" C ILE A 171 " pdb=" N TRP A 172 " pdb=" CA TRP A 172 " ideal model delta harmonic sigma weight residual 180.00 -162.09 -17.91 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ILE B 171 " pdb=" C ILE B 171 " pdb=" N TRP B 172 " pdb=" CA TRP B 172 " ideal model delta harmonic sigma weight residual -180.00 -162.10 -17.90 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA TRP A 172 " pdb=" C TRP A 172 " pdb=" N PRO A 173 " pdb=" CA PRO A 173 " ideal model delta harmonic sigma weight residual -180.00 -162.64 -17.36 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 5665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 796 0.065 - 0.130: 138 0.130 - 0.194: 3 0.194 - 0.259: 0 0.259 - 0.324: 1 Chirality restraints: 938 Sorted by residual: chirality pdb=" CA GLU A 298 " pdb=" N GLU A 298 " pdb=" C GLU A 298 " pdb=" CB GLU A 298 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA GLN A 219 " pdb=" N GLN A 219 " pdb=" C GLN A 219 " pdb=" CB GLN A 219 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA LYS B 91 " pdb=" N LYS B 91 " pdb=" C LYS B 91 " pdb=" CB LYS B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 935 not shown) Planarity restraints: 1730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 256 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C PHE A 256 " 0.031 2.00e-02 2.50e+03 pdb=" O PHE A 256 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS A 257 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 256 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C PHE B 256 " -0.031 2.00e-02 2.50e+03 pdb=" O PHE B 256 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS B 257 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 219 " 0.012 2.00e-02 2.50e+03 1.28e-02 2.44e+00 pdb=" CD GLN A 219 " -0.000 2.00e-02 2.50e+03 pdb=" OE1 GLN A 219 " -0.012 2.00e-02 2.50e+03 pdb=" NE2 GLN A 219 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 219 " -0.018 2.00e-02 2.50e+03 pdb="HE22 GLN A 219 " 0.019 2.00e-02 2.50e+03 ... (remaining 1727 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 358 2.14 - 2.75: 22490 2.75 - 3.37: 35500 3.37 - 3.98: 45493 3.98 - 4.60: 72667 Nonbonded interactions: 176508 Sorted by model distance: nonbonded pdb=" O ALA B 68 " pdb=" HG1 THR B 72 " model vdw 1.524 2.450 nonbonded pdb=" O ALA A 68 " pdb=" HG1 THR A 72 " model vdw 1.524 2.450 nonbonded pdb=" O ILE B 300 " pdb=" HG SER B 303 " model vdw 1.534 2.450 nonbonded pdb=" O ILE A 300 " pdb=" HG SER A 303 " model vdw 1.534 2.450 nonbonded pdb=" O ALA A 129 " pdb="HD22 ASN A 133 " model vdw 1.604 2.450 ... (remaining 176503 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.660 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: 0.210 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.780 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 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 : 0.004 0.056 5976 Z= 0.258 Angle : 0.570 5.555 8142 Z= 0.321 Chirality : 0.043 0.324 938 Planarity : 0.004 0.026 1010 Dihedral : 10.417 78.799 2082 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.34 % Allowed : 2.20 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.31), residues: 762 helix: 1.96 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -0.30 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 39 HIS 0.002 0.001 HIS B 212 PHE 0.018 0.001 PHE A 256 TYR 0.007 0.001 TYR B 312 ARG 0.002 0.000 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 162 average time/residue: 1.7579 time to fit residues: 304.3869 Evaluate side-chains 135 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain B residue 28 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 59 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS A 215 ASN A 276 ASN A 350 ASN B 212 HIS B 276 ASN B 350 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5976 Z= 0.277 Angle : 0.578 5.340 8142 Z= 0.311 Chirality : 0.043 0.134 938 Planarity : 0.005 0.045 1010 Dihedral : 5.277 70.261 857 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.03 % Allowed : 10.00 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.31), residues: 762 helix: 1.67 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -0.05 (0.44), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 39 HIS 0.003 0.001 HIS A 339 PHE 0.015 0.002 PHE B 195 TYR 0.019 0.002 TYR A 312 ARG 0.005 0.001 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.6613 (OUTLIER) cc_final: 0.5744 (mpt) outliers start: 12 outliers final: 2 residues processed: 136 average time/residue: 2.0076 time to fit residues: 290.0616 Evaluate side-chains 133 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain B residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.0970 chunk 57 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS A 215 ASN A 276 ASN A 350 ASN B 212 HIS B 276 ASN B 350 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5976 Z= 0.245 Angle : 0.537 5.266 8142 Z= 0.286 Chirality : 0.041 0.121 938 Planarity : 0.005 0.042 1010 Dihedral : 4.967 61.741 855 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.86 % Allowed : 11.02 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.31), residues: 762 helix: 1.57 (0.22), residues: 516 sheet: None (None), residues: 0 loop : 0.35 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 39 HIS 0.002 0.001 HIS B 339 PHE 0.014 0.001 PHE B 195 TYR 0.024 0.002 TYR B 312 ARG 0.005 0.001 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 VAL cc_start: 0.8380 (t) cc_final: 0.6326 (t) REVERT: A 284 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.5461 (mpm) REVERT: B 380 ASP cc_start: 0.7092 (t0) cc_final: 0.6890 (t0) outliers start: 11 outliers final: 3 residues processed: 133 average time/residue: 1.9277 time to fit residues: 272.8806 Evaluate side-chains 127 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 250 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 350 ASN B 276 ASN B 350 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5976 Z= 0.259 Angle : 0.543 5.312 8142 Z= 0.289 Chirality : 0.041 0.127 938 Planarity : 0.005 0.043 1010 Dihedral : 4.770 49.848 855 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.03 % Allowed : 12.20 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.31), residues: 762 helix: 1.52 (0.22), residues: 516 sheet: None (None), residues: 0 loop : 0.30 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 39 HIS 0.003 0.001 HIS A 339 PHE 0.015 0.001 PHE A 344 TYR 0.015 0.002 TYR B 312 ARG 0.006 0.001 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7759 (mm) REVERT: A 315 HIS cc_start: 0.6371 (OUTLIER) cc_final: 0.6037 (t70) REVERT: B 215 ASN cc_start: 0.6708 (m-40) cc_final: 0.6454 (m110) REVERT: B 380 ASP cc_start: 0.7111 (t0) cc_final: 0.6842 (t0) outliers start: 12 outliers final: 3 residues processed: 135 average time/residue: 1.9514 time to fit residues: 281.6098 Evaluate side-chains 133 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 280 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 350 ASN B 276 ASN B 315 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5976 Z= 0.232 Angle : 0.530 5.221 8142 Z= 0.282 Chirality : 0.041 0.121 938 Planarity : 0.005 0.043 1010 Dihedral : 4.461 39.363 855 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.69 % Allowed : 13.05 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.31), residues: 762 helix: 1.54 (0.23), residues: 518 sheet: None (None), residues: 0 loop : 0.46 (0.44), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 39 HIS 0.006 0.001 HIS B 315 PHE 0.014 0.001 PHE B 195 TYR 0.019 0.002 TYR B 312 ARG 0.004 0.001 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 HIS cc_start: 0.6345 (OUTLIER) cc_final: 0.6082 (t70) REVERT: A 380 ASP cc_start: 0.6855 (t0) cc_final: 0.6505 (t0) REVERT: B 312 TYR cc_start: 0.7403 (t80) cc_final: 0.7153 (t80) REVERT: B 380 ASP cc_start: 0.7112 (t0) cc_final: 0.6800 (t0) outliers start: 10 outliers final: 3 residues processed: 131 average time/residue: 1.9177 time to fit residues: 267.3157 Evaluate side-chains 130 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 250 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.0020 chunk 73 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 70 optimal weight: 0.1980 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 276 ASN A 350 ASN B 276 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5976 Z= 0.272 Angle : 0.550 5.379 8142 Z= 0.296 Chirality : 0.042 0.142 938 Planarity : 0.005 0.043 1010 Dihedral : 4.405 36.245 855 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.69 % Allowed : 13.90 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.31), residues: 762 helix: 1.44 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.48 (0.45), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 39 HIS 0.003 0.001 HIS A 339 PHE 0.014 0.001 PHE B 195 TYR 0.016 0.002 TYR B 312 ARG 0.006 0.001 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 HIS cc_start: 0.6366 (OUTLIER) cc_final: 0.6116 (t70) REVERT: A 380 ASP cc_start: 0.6817 (t0) cc_final: 0.6429 (t0) REVERT: B 9 LEU cc_start: 0.7307 (mm) cc_final: 0.7086 (mt) REVERT: B 380 ASP cc_start: 0.7067 (t0) cc_final: 0.6721 (t0) outliers start: 10 outliers final: 1 residues processed: 131 average time/residue: 1.9211 time to fit residues: 268.6941 Evaluate side-chains 126 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain B residue 250 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 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 58 ASN A 276 ASN B 215 ASN B 276 ASN B 315 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5976 Z= 0.282 Angle : 0.553 5.321 8142 Z= 0.296 Chirality : 0.042 0.129 938 Planarity : 0.005 0.043 1010 Dihedral : 4.066 17.724 852 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.53 % Allowed : 14.41 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.31), residues: 762 helix: 1.42 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.45 (0.45), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 269 HIS 0.008 0.001 HIS B 315 PHE 0.013 0.001 PHE B 195 TYR 0.019 0.002 TYR B 312 ARG 0.003 0.001 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 HIS cc_start: 0.6331 (OUTLIER) cc_final: 0.6071 (t70) REVERT: A 380 ASP cc_start: 0.6818 (t0) cc_final: 0.6406 (t0) REVERT: B 380 ASP cc_start: 0.7033 (t0) cc_final: 0.6669 (t0) outliers start: 9 outliers final: 2 residues processed: 134 average time/residue: 1.8382 time to fit residues: 262.4879 Evaluate side-chains 129 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 250 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 276 ASN B 215 ASN B 276 ASN B 315 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5976 Z= 0.350 Angle : 0.584 5.534 8142 Z= 0.318 Chirality : 0.043 0.137 938 Planarity : 0.006 0.067 1010 Dihedral : 4.234 18.387 852 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.53 % Allowed : 14.07 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.31), residues: 762 helix: 1.30 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.35 (0.46), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 269 HIS 0.004 0.001 HIS B 315 PHE 0.014 0.001 PHE B 195 TYR 0.020 0.002 TYR A 198 ARG 0.010 0.001 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 HIS cc_start: 0.6342 (OUTLIER) cc_final: 0.6085 (t70) outliers start: 9 outliers final: 1 residues processed: 131 average time/residue: 1.9041 time to fit residues: 265.7045 Evaluate side-chains 127 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain B residue 46 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 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 58 ASN A 276 ASN B 58 ASN B 276 ASN B 315 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5976 Z= 0.239 Angle : 0.548 5.350 8142 Z= 0.294 Chirality : 0.041 0.135 938 Planarity : 0.005 0.050 1010 Dihedral : 4.103 18.129 852 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.02 % Allowed : 15.25 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.32), residues: 762 helix: 1.48 (0.23), residues: 520 sheet: None (None), residues: 0 loop : 0.57 (0.46), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 269 HIS 0.004 0.001 HIS B 315 PHE 0.013 0.001 PHE A 195 TYR 0.017 0.002 TYR A 198 ARG 0.007 0.001 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 VAL cc_start: 0.8541 (t) cc_final: 0.6821 (t) REVERT: A 284 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.5390 (mpm) REVERT: A 315 HIS cc_start: 0.6256 (OUTLIER) cc_final: 0.5958 (t70) REVERT: B 9 LEU cc_start: 0.7249 (mm) cc_final: 0.7034 (mt) outliers start: 6 outliers final: 0 residues processed: 132 average time/residue: 1.8453 time to fit residues: 259.4279 Evaluate side-chains 128 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 315 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 276 ASN B 58 ASN B 276 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5976 Z= 0.268 Angle : 0.555 5.405 8142 Z= 0.298 Chirality : 0.042 0.136 938 Planarity : 0.005 0.053 1010 Dihedral : 4.111 18.010 852 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.51 % Allowed : 16.10 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.31), residues: 762 helix: 1.46 (0.23), residues: 522 sheet: None (None), residues: 0 loop : 0.42 (0.46), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 172 HIS 0.002 0.001 HIS A 339 PHE 0.013 0.001 PHE A 195 TYR 0.019 0.002 TYR B 188 ARG 0.007 0.001 ARG A 277 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 129 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 VAL cc_start: 0.8545 (t) cc_final: 0.6896 (t) REVERT: A 284 MET cc_start: 0.6660 (OUTLIER) cc_final: 0.5396 (mpm) REVERT: A 315 HIS cc_start: 0.6258 (OUTLIER) cc_final: 0.5984 (t70) REVERT: B 9 LEU cc_start: 0.7308 (mm) cc_final: 0.7106 (mt) outliers start: 3 outliers final: 0 residues processed: 131 average time/residue: 1.8702 time to fit residues: 261.3073 Evaluate side-chains 131 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 315 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN B 58 ASN B 276 ASN B 315 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.156110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.147722 restraints weight = 21075.259| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.34 r_work: 0.3936 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 5976 Z= 0.482 Angle : 0.644 5.721 8142 Z= 0.355 Chirality : 0.047 0.159 938 Planarity : 0.006 0.072 1010 Dihedral : 4.470 17.672 852 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.68 % Allowed : 16.10 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.31), residues: 762 helix: 1.06 (0.22), residues: 518 sheet: None (None), residues: 0 loop : 0.07 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 214 HIS 0.009 0.002 HIS B 315 PHE 0.017 0.002 PHE A 195 TYR 0.022 0.002 TYR A 198 ARG 0.009 0.001 ARG A 277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5324.88 seconds wall clock time: 96 minutes 6.27 seconds (5766.27 seconds total)