Starting phenix.real_space_refine on Thu Jul 18 20:38:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xco_38249/07_2024/8xco_38249.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xco_38249/07_2024/8xco_38249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xco_38249/07_2024/8xco_38249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xco_38249/07_2024/8xco_38249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xco_38249/07_2024/8xco_38249.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xco_38249/07_2024/8xco_38249.cif" } resolution = 2.64 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2115 2.51 5 N 565 2.21 5 O 638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 5": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3335 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3273 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 3321 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 62 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1, 'water': 14} Link IDs: {None: 14} Time building chain proxies: 4.40, per 1000 atoms: 1.32 Number of scatterers: 3335 At special positions: 0 Unit cell: (69.936, 68.432, 73.696, 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 14 16.00 P 3 15.00 O 638 8.00 N 565 7.00 C 2115 6.00 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 - 3.50 Amino acid : False - 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: 1.39 Conformation dependent library (CDL) restraints added in 1.2 seconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 54.6% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.525A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 164 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.503A pdb=" N VAL A 173 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 365 through 392 removed outlier: 3.520A pdb=" N THR A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.691A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.691A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 279 removed outlier: 6.405A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 197 hydrogen bonds defined for protein. 569 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.95 Time building geometry restraints manager: 1.53 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: 1068 1.34 - 1.46: 583 1.46 - 1.57: 1720 1.57 - 1.69: 3 1.69 - 1.80: 27 Bond restraints: 3401 Sorted by residual: bond pdb=" C TRP A 89 " pdb=" CA BTRP A 89 " ideal model delta sigma weight residual 1.524 1.616 -0.092 1.29e-02 6.01e+03 5.12e+01 bond pdb=" O1N NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.477 1.548 -0.071 1.00e-02 1.00e+04 5.06e+01 bond pdb=" C GLY A 183 " pdb=" N SER A 184 " ideal model delta sigma weight residual 1.331 1.436 -0.105 1.51e-02 4.39e+03 4.85e+01 bond pdb=" O2B NDP A 500 " pdb=" P2B NDP A 500 " ideal model delta sigma weight residual 1.833 1.569 0.264 3.80e-02 6.93e+02 4.84e+01 bond pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.757 1.559 0.198 3.50e-02 8.16e+02 3.22e+01 ... (remaining 3396 not shown) Histogram of bond angle deviations from ideal: 96.08 - 103.66: 58 103.66 - 111.25: 1413 111.25 - 118.83: 1354 118.83 - 126.42: 1715 126.42 - 134.00: 83 Bond angle restraints: 4623 Sorted by residual: angle pdb=" C1D NDP A 500 " pdb=" O4D NDP A 500 " pdb=" C4D NDP A 500 " ideal model delta sigma weight residual 105.41 127.47 -22.06 2.71e+00 1.37e-01 6.65e+01 angle pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " ideal model delta sigma weight residual 103.84 119.18 -15.34 1.91e+00 2.73e-01 6.42e+01 angle pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 107.74 122.34 -14.60 1.95e+00 2.62e-01 5.58e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 109.47 7.99 1.17e+00 7.36e-01 4.69e+01 angle pdb=" O2X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.33 108.95 8.38 1.48e+00 4.57e-01 3.21e+01 ... (remaining 4618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.83: 1835 23.83 - 47.67: 137 47.67 - 71.50: 36 71.50 - 95.34: 4 95.34 - 119.17: 1 Dihedral angle restraints: 2013 sinusoidal: 820 harmonic: 1193 Sorted by residual: dihedral pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " ideal model delta sinusoidal sigma weight residual 175.04 55.87 119.17 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" CA ASP A 256 " pdb=" CB ASP A 256 " pdb=" CG ASP A 256 " pdb=" OD1 ASP A 256 " ideal model delta sinusoidal sigma weight residual -30.00 -86.85 56.85 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASN A 319 " pdb=" CB ASN A 319 " pdb=" CG ASN A 319 " pdb=" OD1 ASN A 319 " ideal model delta sinusoidal sigma weight residual -90.00 -159.73 69.73 2 2.00e+01 2.50e-03 1.06e+01 ... (remaining 2010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 433 0.079 - 0.158: 59 0.158 - 0.236: 4 0.236 - 0.315: 3 0.315 - 0.394: 3 Chirality restraints: 502 Sorted by residual: chirality pdb=" C4D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" C5D NDP A 500 " pdb=" O4D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.32 -0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" C2D NDP A 500 " pdb=" C1D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" O2D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.34 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C1B NDP A 500 " pdb=" C2B NDP A 500 " pdb=" N9A NDP A 500 " pdb=" O4B NDP A 500 " both_signs ideal model delta sigma weight residual False 2.59 2.24 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 499 not shown) Planarity restraints: 587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 500 " -0.104 2.00e-02 2.50e+03 1.98e-01 3.92e+02 pdb=" C5N NDP A 500 " 0.256 2.00e-02 2.50e+03 pdb=" C6N NDP A 500 " -0.262 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " 0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 500 " 0.059 2.00e-02 2.50e+03 1.00e-01 1.26e+02 pdb=" C3N NDP A 500 " 0.166 2.00e-02 2.50e+03 pdb=" C4N NDP A 500 " -0.038 2.00e-02 2.50e+03 pdb=" C7N NDP A 500 " -0.106 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 143 " -0.061 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO A 144 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " -0.050 5.00e-02 4.00e+02 ... (remaining 584 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 1329 2.92 - 3.41: 3324 3.41 - 3.91: 5836 3.91 - 4.40: 6734 4.40 - 4.90: 11087 Nonbonded interactions: 28310 Sorted by model distance: nonbonded pdb=" OH TYR A 352 " pdb=" O HOH A 601 " model vdw 2.424 2.440 nonbonded pdb=" NE ARG A 65 " pdb=" O HOH A 602 " model vdw 2.446 2.520 nonbonded pdb=" O ILE A 174 " pdb=" NZ LYS A 177 " model vdw 2.505 2.520 nonbonded pdb=" OD2 ASP A 47 " pdb=" OG SER A 116 " model vdw 2.516 2.440 nonbonded pdb=" O2B NDP A 500 " pdb=" O3B NDP A 500 " model vdw 2.532 2.432 ... (remaining 28305 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.50 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: 0.010 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.960 Find NCS groups from input model: 0.040 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:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 0.009 0.264 3401 Z= 0.586 Angle : 1.129 22.060 4623 Z= 0.602 Chirality : 0.060 0.394 502 Planarity : 0.011 0.198 587 Dihedral : 17.486 119.173 1253 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 6.78 % Allowed : 4.72 % Favored : 88.50 % 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: 0.92 (0.42), residues: 415 helix: 1.60 (0.35), residues: 211 sheet: -0.20 (0.69), residues: 66 loop : -0.44 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 HIS 0.001 0.000 HIS A 75 PHE 0.010 0.001 PHE A 341 TYR 0.004 0.001 TYR A 101 ARG 0.001 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 0.416 Fit side-chains REVERT: A 149 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8638 (p0) REVERT: A 263 TRP cc_start: 0.8650 (t-100) cc_final: 0.8322 (t-100) REVERT: A 310 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8028 (mttp) outliers start: 23 outliers final: 1 residues processed: 105 average time/residue: 1.2864 time to fit residues: 138.9850 Evaluate side-chains 57 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 310 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN A 337 GLN A 388 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3401 Z= 0.162 Angle : 0.491 6.908 4623 Z= 0.251 Chirality : 0.042 0.146 502 Planarity : 0.005 0.069 587 Dihedral : 7.547 115.513 471 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.95 % Allowed : 17.11 % Favored : 79.94 % 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: 1.92 (0.44), residues: 415 helix: 2.33 (0.36), residues: 213 sheet: 0.12 (0.70), residues: 68 loop : 0.26 (0.60), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 30 HIS 0.002 0.001 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.009 0.001 TYR A 250 ARG 0.005 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.452 Fit side-chains REVERT: A 262 LYS cc_start: 0.8636 (tttp) cc_final: 0.8362 (tttm) outliers start: 10 outliers final: 4 residues processed: 65 average time/residue: 1.3130 time to fit residues: 87.8625 Evaluate side-chains 61 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 307 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 0.1980 chunk 36 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3401 Z= 0.225 Angle : 0.486 5.437 4623 Z= 0.259 Chirality : 0.043 0.151 502 Planarity : 0.005 0.058 587 Dihedral : 6.561 94.035 466 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.65 % Allowed : 17.11 % Favored : 80.24 % 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: 1.78 (0.43), residues: 415 helix: 2.24 (0.35), residues: 213 sheet: 0.16 (0.69), residues: 70 loop : 0.09 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 364 HIS 0.003 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.014 0.001 TYR A 363 ARG 0.004 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.405 Fit side-chains REVERT: A 90 MET cc_start: 0.9002 (mmm) cc_final: 0.8768 (mmm) REVERT: A 312 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8286 (mtpt) REVERT: A 392 ASN cc_start: 0.8793 (t0) cc_final: 0.8350 (t0) outliers start: 9 outliers final: 3 residues processed: 57 average time/residue: 1.2805 time to fit residues: 75.2272 Evaluate side-chains 53 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 312 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.0270 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3401 Z= 0.122 Angle : 0.432 5.264 4623 Z= 0.226 Chirality : 0.041 0.126 502 Planarity : 0.005 0.051 587 Dihedral : 6.104 81.576 466 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.77 % Allowed : 18.29 % Favored : 79.94 % 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: 2.00 (0.43), residues: 415 helix: 2.53 (0.35), residues: 214 sheet: 0.29 (0.69), residues: 68 loop : -0.09 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 263 HIS 0.002 0.000 HIS A 267 PHE 0.007 0.001 PHE A 381 TYR 0.008 0.001 TYR A 250 ARG 0.004 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.362 Fit side-chains REVERT: A 78 GLU cc_start: 0.7793 (tp30) cc_final: 0.7591 (mm-30) REVERT: A 312 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8262 (mtpt) REVERT: A 392 ASN cc_start: 0.8741 (t0) cc_final: 0.8307 (t0) outliers start: 6 outliers final: 2 residues processed: 60 average time/residue: 1.1147 time to fit residues: 68.9958 Evaluate side-chains 55 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 312 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3401 Z= 0.135 Angle : 0.430 5.935 4623 Z= 0.225 Chirality : 0.041 0.126 502 Planarity : 0.004 0.047 587 Dihedral : 5.954 76.812 466 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.06 % Allowed : 18.29 % Favored : 79.65 % 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: 2.05 (0.43), residues: 415 helix: 2.57 (0.35), residues: 214 sheet: 0.39 (0.69), residues: 68 loop : -0.11 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 263 HIS 0.001 0.001 HIS A 388 PHE 0.007 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.004 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.428 Fit side-chains REVERT: A 149 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.7983 (p0) REVERT: A 312 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8223 (mtpt) REVERT: A 392 ASN cc_start: 0.8736 (t0) cc_final: 0.8302 (t0) outliers start: 7 outliers final: 2 residues processed: 58 average time/residue: 1.0955 time to fit residues: 65.6546 Evaluate side-chains 54 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 312 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.0040 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 0.0060 chunk 22 optimal weight: 0.8980 overall best weight: 1.3610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3401 Z= 0.165 Angle : 0.445 6.869 4623 Z= 0.233 Chirality : 0.042 0.131 502 Planarity : 0.004 0.045 587 Dihedral : 5.812 68.034 466 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.36 % Allowed : 18.29 % Favored : 79.35 % 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: 2.01 (0.43), residues: 415 helix: 2.57 (0.35), residues: 214 sheet: 0.32 (0.68), residues: 68 loop : -0.16 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 263 HIS 0.001 0.001 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.009 0.001 TYR A 363 ARG 0.004 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 312 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8222 (mtpt) REVERT: A 392 ASN cc_start: 0.8747 (t0) cc_final: 0.8317 (t0) outliers start: 8 outliers final: 5 residues processed: 57 average time/residue: 1.0601 time to fit residues: 62.5619 Evaluate side-chains 57 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 312 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.0470 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 0.0070 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.3900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3401 Z= 0.165 Angle : 0.442 6.882 4623 Z= 0.232 Chirality : 0.042 0.128 502 Planarity : 0.004 0.045 587 Dihedral : 5.397 57.822 466 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.36 % Allowed : 18.88 % Favored : 78.76 % 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: 1.93 (0.43), residues: 415 helix: 2.54 (0.35), residues: 214 sheet: 0.25 (0.67), residues: 70 loop : -0.24 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 263 HIS 0.001 0.001 HIS A 267 PHE 0.009 0.001 PHE A 381 TYR 0.009 0.001 TYR A 363 ARG 0.003 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.504 Fit side-chains REVERT: A 149 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8322 (p0) REVERT: A 263 TRP cc_start: 0.8568 (t-100) cc_final: 0.7702 (t-100) REVERT: A 312 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8209 (mtpt) REVERT: A 392 ASN cc_start: 0.8742 (t0) cc_final: 0.8323 (t0) outliers start: 8 outliers final: 3 residues processed: 57 average time/residue: 1.1125 time to fit residues: 65.6540 Evaluate side-chains 54 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 312 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3401 Z= 0.148 Angle : 0.437 7.057 4623 Z= 0.228 Chirality : 0.041 0.124 502 Planarity : 0.004 0.045 587 Dihedral : 4.785 46.824 466 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.77 % Allowed : 19.47 % Favored : 78.76 % 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: 1.98 (0.43), residues: 415 helix: 2.61 (0.35), residues: 214 sheet: 0.16 (0.67), residues: 70 loop : -0.20 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 263 HIS 0.001 0.001 HIS A 267 PHE 0.008 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.003 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 312 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8188 (mtpt) REVERT: A 392 ASN cc_start: 0.8732 (t0) cc_final: 0.8319 (t0) outliers start: 6 outliers final: 2 residues processed: 52 average time/residue: 1.0724 time to fit residues: 57.8135 Evaluate side-chains 52 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 312 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 0.0980 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 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 149 ASN A 319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3401 Z= 0.127 Angle : 0.430 7.191 4623 Z= 0.223 Chirality : 0.041 0.123 502 Planarity : 0.004 0.047 587 Dihedral : 4.391 44.098 464 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.59 % Allowed : 20.35 % Favored : 79.06 % 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: 2.06 (0.43), residues: 415 helix: 2.68 (0.35), residues: 214 sheet: 0.20 (0.67), residues: 70 loop : -0.17 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 263 HIS 0.001 0.000 HIS A 388 PHE 0.007 0.001 PHE A 381 TYR 0.007 0.001 TYR A 363 ARG 0.003 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.418 Fit side-chains REVERT: A 312 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8193 (mtpt) REVERT: A 392 ASN cc_start: 0.8717 (t0) cc_final: 0.8310 (t0) outliers start: 2 outliers final: 0 residues processed: 50 average time/residue: 1.0708 time to fit residues: 55.5368 Evaluate side-chains 47 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 0.0870 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 0.0270 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3401 Z= 0.128 Angle : 0.424 7.261 4623 Z= 0.221 Chirality : 0.041 0.123 502 Planarity : 0.004 0.046 587 Dihedral : 4.345 43.584 464 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.59 % Allowed : 20.65 % Favored : 78.76 % 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: 2.08 (0.43), residues: 415 helix: 2.66 (0.35), residues: 214 sheet: 0.30 (0.67), residues: 70 loop : -0.15 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 263 HIS 0.001 0.001 HIS A 267 PHE 0.007 0.001 PHE A 381 TYR 0.007 0.001 TYR A 363 ARG 0.003 0.000 ARG A 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 312 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8183 (mtpt) REVERT: A 392 ASN cc_start: 0.8719 (t0) cc_final: 0.8311 (t0) outliers start: 2 outliers final: 0 residues processed: 50 average time/residue: 1.1541 time to fit residues: 60.0100 Evaluate side-chains 50 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.103824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.069575 restraints weight = 11488.696| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 2.58 r_work: 0.2506 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2382 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2361 r_free = 0.2361 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2361 r_free = 0.2361 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3401 Z= 0.350 Angle : 0.530 6.795 4623 Z= 0.280 Chirality : 0.046 0.157 502 Planarity : 0.005 0.046 587 Dihedral : 4.677 42.054 464 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.47 % Allowed : 19.76 % Favored : 78.76 % 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: 1.74 (0.43), residues: 415 helix: 2.28 (0.34), residues: 213 sheet: 0.17 (0.67), residues: 72 loop : -0.11 (0.57), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 364 HIS 0.003 0.001 HIS A 394 PHE 0.011 0.002 PHE A 381 TYR 0.015 0.002 TYR A 363 ARG 0.003 0.001 ARG A 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1854.31 seconds wall clock time: 33 minutes 15.18 seconds (1995.18 seconds total)