Starting phenix.real_space_refine on Mon May 6 16:59:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6t_28890/05_2024/8f6t_28890_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6t_28890/05_2024/8f6t_28890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6t_28890/05_2024/8f6t_28890.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6t_28890/05_2024/8f6t_28890.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6t_28890/05_2024/8f6t_28890_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6t_28890/05_2024/8f6t_28890_updated.pdb" } resolution = 2.76 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= 0.008 sd= 0.114 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 Fe 3 7.16 5 S 11 5.16 5 C 2261 2.51 5 N 604 2.21 5 O 594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A ARG 433": "NH1" <-> "NH2" Residue "A GLU 434": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 3473 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3473 Unusual residues: {' FE': 3, 'D12': 1} Classifications: {'peptide': 428, 'undetermined': 4} Link IDs: {'PTRANS': 30, 'TRANS': 397, None: 4} Not linked: pdbres="ALA A 467 " pdbres=" FE A 501 " Not linked: pdbres=" FE A 501 " pdbres=" FE A 502 " Not linked: pdbres=" FE A 502 " pdbres=" FE A 503 " Not linked: pdbres=" FE A 503 " pdbres="D12 A 504 " Chain breaks: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3074 SG CYS A 418 40.499 23.954 46.620 1.00125.12 S ATOM 3095 SG CYS A 421 40.898 27.411 46.825 1.00127.79 S ATOM 3331 SG CYS A 451 38.727 26.710 49.011 1.00124.73 S ATOM 3352 SG CYS A 454 37.613 26.470 45.458 1.00120.95 S Time building chain proxies: 3.10, per 1000 atoms: 0.89 Number of scatterers: 3473 At special positions: 0 Unit cell: (65.268, 81.252, 75.924, 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) Fe 3 26.01 S 11 16.00 O 594 8.00 N 604 7.00 C 2261 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: 1.56 Conformation dependent library (CDL) restraints added in 1.3 seconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 796 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 0 sheets defined 56.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.613A pdb=" N LEU A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Proline residue: A 25 - end of helix Proline residue: A 28 - end of helix removed outlier: 4.106A pdb=" N THR A 41 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 47 Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 58 through 64 removed outlier: 4.890A pdb=" N TRP A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 82 removed outlier: 4.258A pdb=" N ALA A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 110 removed outlier: 4.041A pdb=" N VAL A 90 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Proline residue: A 95 - end of helix removed outlier: 3.854A pdb=" N TYR A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ALA A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 140 Processing helix chain 'A' and resid 145 through 154 removed outlier: 3.664A pdb=" N TRP A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 removed outlier: 4.773A pdb=" N HIS A 167 " --> pdb=" O PHE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 194 through 215 Processing helix chain 'A' and resid 226 through 244 removed outlier: 3.910A pdb=" N MET A 233 " --> pdb=" O GLN A 229 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 271 removed outlier: 3.604A pdb=" N ILE A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 313 through 316 No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 343 through 346 No H-bonds generated for 'chain 'A' and resid 343 through 346' Processing helix chain 'A' and resid 348 through 362 Proline residue: A 357 - end of helix Processing helix chain 'A' and resid 374 through 384 removed outlier: 5.467A pdb=" N ALA A 378 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A 379 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP A 384 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' 129 hydrogen bonds defined for protein. 318 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: 0.86 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1104 1.34 - 1.46: 717 1.46 - 1.57: 1749 1.57 - 1.69: 0 1.69 - 1.81: 15 Bond restraints: 3585 Sorted by residual: bond pdb=" CA HIS A 314 " pdb=" C HIS A 314 " ideal model delta sigma weight residual 1.523 1.512 0.011 1.30e-02 5.92e+03 7.03e-01 bond pdb=" CG PRO A 25 " pdb=" CD PRO A 25 " ideal model delta sigma weight residual 1.503 1.478 0.025 3.40e-02 8.65e+02 5.39e-01 bond pdb=" CG1 ILE A 131 " pdb=" CD1 ILE A 131 " ideal model delta sigma weight residual 1.513 1.485 0.028 3.90e-02 6.57e+02 5.31e-01 bond pdb=" N GLU A 271 " pdb=" CA GLU A 271 " ideal model delta sigma weight residual 1.459 1.468 -0.009 1.19e-02 7.06e+03 5.20e-01 bond pdb=" C ILE A 343 " pdb=" N PRO A 344 " ideal model delta sigma weight residual 1.334 1.350 -0.017 2.34e-02 1.83e+03 5.02e-01 ... (remaining 3580 not shown) Histogram of bond angle deviations from ideal: 99.75 - 106.60: 151 106.60 - 113.45: 1905 113.45 - 120.30: 1391 120.30 - 127.15: 1375 127.15 - 134.00: 76 Bond angle restraints: 4898 Sorted by residual: angle pdb=" N ASP A 453 " pdb=" CA ASP A 453 " pdb=" C ASP A 453 " ideal model delta sigma weight residual 114.56 110.05 4.51 1.27e+00 6.20e-01 1.26e+01 angle pdb=" CA ASP A 453 " pdb=" C ASP A 453 " pdb=" N CYS A 454 " ideal model delta sigma weight residual 119.26 116.45 2.81 1.14e+00 7.69e-01 6.09e+00 angle pdb=" C ASN A 168 " pdb=" N ARG A 169 " pdb=" CA ARG A 169 " ideal model delta sigma weight residual 121.99 118.70 3.29 1.56e+00 4.11e-01 4.46e+00 angle pdb=" CA ASP A 453 " pdb=" C ASP A 453 " pdb=" O ASP A 453 " ideal model delta sigma weight residual 118.55 120.78 -2.23 1.14e+00 7.69e-01 3.83e+00 angle pdb=" N PRO A 374 " pdb=" CA PRO A 374 " pdb=" C PRO A 374 " ideal model delta sigma weight residual 110.70 112.87 -2.17 1.22e+00 6.72e-01 3.17e+00 ... (remaining 4893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 1849 16.14 - 32.29: 184 32.29 - 48.43: 38 48.43 - 64.57: 2 64.57 - 80.71: 1 Dihedral angle restraints: 2074 sinusoidal: 830 harmonic: 1244 Sorted by residual: dihedral pdb=" CA LEU A 367 " pdb=" C LEU A 367 " pdb=" N THR A 368 " pdb=" CA THR A 368 " ideal model delta harmonic sigma weight residual 180.00 161.77 18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PRO A 59 " pdb=" C PRO A 59 " pdb=" N LEU A 60 " pdb=" CA LEU A 60 " ideal model delta harmonic sigma weight residual 180.00 162.65 17.35 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA TYR A 160 " pdb=" C TYR A 160 " pdb=" N GLY A 161 " pdb=" CA GLY A 161 " ideal model delta harmonic sigma weight residual 180.00 -163.69 -16.31 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 2071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 267 0.027 - 0.053: 151 0.053 - 0.080: 64 0.080 - 0.107: 27 0.107 - 0.134: 7 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA ARG A 169 " pdb=" N ARG A 169 " pdb=" C ARG A 169 " pdb=" CB ARG A 169 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA VAL A 347 " pdb=" N VAL A 347 " pdb=" C VAL A 347 " pdb=" CB VAL A 347 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE A 445 " pdb=" N ILE A 445 " pdb=" C ILE A 445 " pdb=" CB ILE A 445 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 513 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 373 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 374 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 374 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 374 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 180 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO A 181 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 440 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 441 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 441 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 441 " 0.019 5.00e-02 4.00e+02 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 52 2.68 - 3.23: 3390 3.23 - 3.79: 5331 3.79 - 4.34: 7214 4.34 - 4.90: 11797 Nonbonded interactions: 27784 Sorted by model distance: nonbonded pdb=" NE2 HIS A 167 " pdb="FE FE A 502 " model vdw 2.119 2.340 nonbonded pdb=" NE2 HIS A 272 " pdb="FE FE A 501 " model vdw 2.163 2.340 nonbonded pdb=" NE2 HIS A 314 " pdb="FE FE A 502 " model vdw 2.167 2.340 nonbonded pdb=" NE2 HIS A 141 " pdb="FE FE A 502 " model vdw 2.198 2.340 nonbonded pdb=" ND2 ASN A 129 " pdb=" OE1 GLN A 256 " model vdw 2.215 2.520 ... (remaining 27779 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=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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 16.310 Find NCS groups from input model: 0.120 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:14.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 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 0.029 3585 Z= 0.281 Angle : 0.629 6.030 4898 Z= 0.344 Chirality : 0.041 0.134 516 Planarity : 0.005 0.049 624 Dihedral : 12.871 80.711 1278 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 0.80 (0.42), residues: 424 helix: 1.16 (0.36), residues: 239 sheet: None (None), residues: 0 loop : -0.22 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 106 HIS 0.007 0.001 HIS A 315 PHE 0.010 0.001 PHE A 26 TYR 0.010 0.001 TYR A 423 ARG 0.004 0.001 ARG A 361 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.334 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 1.1016 time to fit residues: 34.8017 Evaluate side-chains 21 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 33 optimal weight: 0.0070 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3585 Z= 0.172 Angle : 0.540 7.495 4898 Z= 0.268 Chirality : 0.038 0.129 516 Planarity : 0.005 0.046 624 Dihedral : 5.352 49.923 485 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.12 % Allowed : 6.70 % Favored : 92.18 % 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: 0.68 (0.42), residues: 424 helix: 1.11 (0.36), residues: 233 sheet: None (None), residues: 0 loop : -0.29 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 351 HIS 0.007 0.001 HIS A 315 PHE 0.009 0.001 PHE A 193 TYR 0.009 0.001 TYR A 160 ARG 0.002 0.000 ARG A 361 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.354 Fit side-chains REVERT: A 42 ASP cc_start: 0.8493 (t0) cc_final: 0.8269 (t0) REVERT: A 226 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7976 (mt-10) REVERT: A 271 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7673 (mt-10) outliers start: 4 outliers final: 1 residues processed: 24 average time/residue: 0.9634 time to fit residues: 24.4612 Evaluate side-chains 21 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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: 0.8436 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3585 Z= 0.195 Angle : 0.521 5.807 4898 Z= 0.260 Chirality : 0.038 0.127 516 Planarity : 0.005 0.045 624 Dihedral : 5.308 55.522 485 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.40 % Allowed : 8.10 % Favored : 90.50 % 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: 0.69 (0.42), residues: 424 helix: 1.07 (0.36), residues: 232 sheet: None (None), residues: 0 loop : -0.21 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 116 HIS 0.005 0.001 HIS A 311 PHE 0.009 0.001 PHE A 163 TYR 0.008 0.001 TYR A 85 ARG 0.004 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.378 Fit side-chains REVERT: A 42 ASP cc_start: 0.8553 (t0) cc_final: 0.8290 (t0) REVERT: A 226 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8005 (mt-10) REVERT: A 271 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7685 (mt-10) outliers start: 5 outliers final: 2 residues processed: 24 average time/residue: 1.0780 time to fit residues: 27.1782 Evaluate side-chains 25 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 288 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 0.0000 chunk 29 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 4 optimal weight: 0.0020 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.0870 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.2570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3585 Z= 0.150 Angle : 0.499 6.039 4898 Z= 0.247 Chirality : 0.036 0.130 516 Planarity : 0.005 0.045 624 Dihedral : 4.991 52.791 485 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.40 % Allowed : 8.66 % Favored : 89.94 % 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: 0.70 (0.42), residues: 424 helix: 1.05 (0.36), residues: 231 sheet: None (None), residues: 0 loop : -0.14 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 349 HIS 0.005 0.001 HIS A 311 PHE 0.009 0.001 PHE A 193 TYR 0.008 0.001 TYR A 85 ARG 0.001 0.000 ARG A 361 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.394 Fit side-chains REVERT: A 42 ASP cc_start: 0.8517 (t0) cc_final: 0.8251 (t0) REVERT: A 226 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: A 271 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7582 (mt-10) outliers start: 5 outliers final: 1 residues processed: 35 average time/residue: 0.9240 time to fit residues: 33.9199 Evaluate side-chains 29 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 226 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 30 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.8407 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3585 Z= 0.164 Angle : 0.500 5.718 4898 Z= 0.245 Chirality : 0.037 0.128 516 Planarity : 0.005 0.044 624 Dihedral : 4.977 55.952 485 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.40 % Allowed : 10.61 % Favored : 87.99 % 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: 0.61 (0.42), residues: 424 helix: 1.15 (0.37), residues: 225 sheet: 0.58 (1.85), residues: 9 loop : -0.44 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 116 HIS 0.004 0.001 HIS A 311 PHE 0.008 0.001 PHE A 163 TYR 0.007 0.001 TYR A 85 ARG 0.004 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 27 time to evaluate : 0.407 Fit side-chains REVERT: A 42 ASP cc_start: 0.8554 (t0) cc_final: 0.8230 (t0) REVERT: A 226 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8083 (mt-10) outliers start: 5 outliers final: 3 residues processed: 28 average time/residue: 0.9606 time to fit residues: 28.2696 Evaluate side-chains 32 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 226 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 4 optimal weight: 0.3980 chunk 23 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3585 Z= 0.154 Angle : 0.494 5.680 4898 Z= 0.243 Chirality : 0.037 0.129 516 Planarity : 0.005 0.044 624 Dihedral : 4.900 57.150 485 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.40 % Allowed : 11.73 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.43), residues: 424 helix: 1.20 (0.37), residues: 225 sheet: 0.58 (1.85), residues: 9 loop : -0.39 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 116 HIS 0.005 0.001 HIS A 311 PHE 0.009 0.001 PHE A 163 TYR 0.007 0.001 TYR A 85 ARG 0.005 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.407 Fit side-chains REVERT: A 42 ASP cc_start: 0.8544 (t0) cc_final: 0.8239 (t0) REVERT: A 226 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8083 (mt-10) REVERT: A 315 HIS cc_start: 0.8784 (OUTLIER) cc_final: 0.8405 (t-90) outliers start: 5 outliers final: 2 residues processed: 33 average time/residue: 0.8407 time to fit residues: 29.3273 Evaluate side-chains 30 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 315 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 7.9990 chunk 23 optimal weight: 0.0770 chunk 35 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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: 0.8393 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3585 Z= 0.159 Angle : 0.517 8.087 4898 Z= 0.247 Chirality : 0.037 0.129 516 Planarity : 0.005 0.044 624 Dihedral : 4.744 52.717 485 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.68 % Allowed : 12.57 % Favored : 85.75 % 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: 0.71 (0.43), residues: 424 helix: 1.22 (0.37), residues: 225 sheet: 0.61 (1.84), residues: 9 loop : -0.38 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 116 HIS 0.005 0.001 HIS A 311 PHE 0.009 0.001 PHE A 163 TYR 0.006 0.001 TYR A 85 ARG 0.005 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.395 Fit side-chains REVERT: A 42 ASP cc_start: 0.8545 (t0) cc_final: 0.8247 (t0) REVERT: A 226 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8075 (mt-10) REVERT: A 315 HIS cc_start: 0.8760 (OUTLIER) cc_final: 0.8481 (t-90) outliers start: 6 outliers final: 2 residues processed: 29 average time/residue: 0.9628 time to fit residues: 29.3201 Evaluate side-chains 30 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 315 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 0.0070 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.0270 chunk 37 optimal weight: 0.0060 chunk 39 optimal weight: 0.0030 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 overall best weight: 0.1882 ------------------------------------------------------------------------------- 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: 0.8350 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 3585 Z= 0.153 Angle : 0.505 6.396 4898 Z= 0.245 Chirality : 0.036 0.129 516 Planarity : 0.004 0.043 624 Dihedral : 4.361 43.159 485 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.84 % Allowed : 13.97 % Favored : 85.20 % 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: 0.76 (0.43), residues: 424 helix: 1.25 (0.37), residues: 225 sheet: 0.60 (1.85), residues: 9 loop : -0.33 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 116 HIS 0.003 0.001 HIS A 315 PHE 0.009 0.001 PHE A 193 TYR 0.006 0.001 TYR A 85 ARG 0.003 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.403 Fit side-chains REVERT: A 42 ASP cc_start: 0.8510 (t0) cc_final: 0.8232 (t0) REVERT: A 226 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7932 (mt-10) outliers start: 3 outliers final: 1 residues processed: 33 average time/residue: 0.7779 time to fit residues: 27.1875 Evaluate side-chains 31 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 235 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.0000 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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: 0.8376 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 3585 Z= 0.166 Angle : 0.507 5.683 4898 Z= 0.246 Chirality : 0.037 0.127 516 Planarity : 0.004 0.043 624 Dihedral : 4.333 41.311 485 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.56 % Allowed : 14.53 % Favored : 84.92 % 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: 0.75 (0.43), residues: 424 helix: 1.23 (0.37), residues: 225 sheet: 0.69 (1.84), residues: 9 loop : -0.33 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 116 HIS 0.002 0.001 HIS A 272 PHE 0.009 0.001 PHE A 163 TYR 0.005 0.001 TYR A 85 ARG 0.005 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.380 Fit side-chains REVERT: A 42 ASP cc_start: 0.8520 (t0) cc_final: 0.8247 (t0) REVERT: A 226 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7903 (mt-10) outliers start: 2 outliers final: 0 residues processed: 28 average time/residue: 0.9208 time to fit residues: 27.1687 Evaluate side-chains 25 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.7687 > 50: distance: 40 - 67: 31.671 distance: 45 - 78: 31.316 distance: 51 - 89: 31.734 distance: 55 - 67: 34.743 distance: 56 - 97: 27.514 distance: 67 - 68: 34.179 distance: 68 - 69: 52.577 distance: 68 - 71: 52.775 distance: 69 - 70: 39.887 distance: 69 - 78: 48.373 distance: 70 - 105: 56.278 distance: 71 - 72: 4.771 distance: 72 - 73: 39.206 distance: 72 - 74: 24.428 distance: 73 - 75: 39.513 distance: 74 - 76: 21.563 distance: 75 - 77: 34.534 distance: 76 - 77: 32.401 distance: 78 - 79: 56.869 distance: 79 - 80: 35.311 distance: 79 - 82: 15.161 distance: 80 - 81: 8.434 distance: 80 - 89: 58.511 distance: 84 - 85: 15.605 distance: 85 - 86: 26.185 distance: 86 - 87: 35.688 distance: 86 - 88: 43.079 distance: 89 - 90: 19.588 distance: 90 - 91: 52.003 distance: 90 - 93: 56.963 distance: 91 - 92: 54.240 distance: 91 - 97: 11.688 distance: 97 - 98: 20.958 distance: 98 - 99: 38.099 distance: 98 - 101: 38.050 distance: 99 - 105: 39.442 distance: 102 - 103: 40.393 distance: 103 - 104: 56.790 distance: 106 - 107: 56.618 distance: 106 - 109: 56.081 distance: 107 - 108: 55.998 distance: 108 - 135: 43.580 distance: 109 - 110: 38.924 distance: 110 - 111: 69.687 distance: 110 - 112: 40.716 distance: 114 - 115: 56.213 distance: 114 - 117: 57.423 distance: 115 - 120: 46.250 distance: 116 - 140: 42.309 distance: 117 - 118: 39.621 distance: 118 - 119: 39.678 distance: 120 - 121: 43.514 distance: 121 - 122: 39.775 distance: 121 - 124: 40.228 distance: 122 - 123: 41.046 distance: 122 - 128: 39.183 distance: 123 - 151: 36.289 distance: 124 - 125: 48.205 distance: 125 - 126: 11.315 distance: 125 - 127: 41.745 distance: 128 - 129: 34.484 distance: 129 - 130: 31.242 distance: 129 - 132: 57.395 distance: 130 - 135: 56.714 distance: 132 - 133: 56.331 distance: 132 - 134: 48.623 distance: 135 - 136: 34.558 distance: 136 - 137: 41.490 distance: 137 - 138: 34.996 distance: 137 - 140: 5.635 distance: 140 - 141: 39.939 distance: 141 - 144: 39.844 distance: 142 - 151: 35.314 distance: 145 - 146: 19.381 distance: 146 - 147: 23.191 distance: 148 - 149: 40.403 distance: 148 - 150: 8.092