Starting phenix.real_space_refine on Fri Apr 5 14:14:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/04_2024/8ex6_28652_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/04_2024/8ex6_28652.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/04_2024/8ex6_28652_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/04_2024/8ex6_28652_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/04_2024/8ex6_28652_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/04_2024/8ex6_28652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/04_2024/8ex6_28652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/04_2024/8ex6_28652_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/04_2024/8ex6_28652_updated.pdb" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 1 5.49 5 S 17 5.16 5 C 2120 2.51 5 N 531 2.21 5 O 553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 497": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3222 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3222 Unusual residues: {'S1P': 1} Classifications: {'peptide': 416, 'undetermined': 1} Link IDs: {'PTRANS': 12, 'TRANS': 403, None: 1} Not linked: pdbres="GLN A 539 " pdbres="S1P A 601 " Chain breaks: 2 Time building chain proxies: 2.22, per 1000 atoms: 0.69 Number of scatterers: 3222 At special positions: 0 Unit cell: (72.039, 69.443, 83.721, 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 17 16.00 P 1 15.00 O 553 8.00 N 531 7.00 C 2120 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: 1.27 Conformation dependent library (CDL) restraints added in 572.0 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 0 sheets defined 88.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 100 through 133 removed outlier: 4.663A pdb=" N VAL A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 164 removed outlier: 3.982A pdb=" N GLN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) Proline residue: A 156 - end of helix removed outlier: 3.526A pdb=" N ASP A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 187 removed outlier: 3.932A pdb=" N PHE A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 221 Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 224 through 256 removed outlier: 4.400A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 4.018A pdb=" N GLN A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 266 through 280 Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 347 Proline residue: A 337 - end of helix Processing helix chain 'A' and resid 361 through 389 removed outlier: 4.259A pdb=" N VAL A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL A 379 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 420 removed outlier: 4.112A pdb=" N PHE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 416 " --> pdb=" O CYS A 412 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 Processing helix chain 'A' and resid 441 through 450 Processing helix chain 'A' and resid 453 through 470 removed outlier: 5.238A pdb=" N ALA A 457 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA A 459 " --> pdb=" O ARG A 456 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 462 " --> pdb=" O ALA A 459 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 470 " --> pdb=" O SER A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 489 Proline residue: A 476 - end of helix Processing helix chain 'A' and resid 494 through 538 removed outlier: 3.982A pdb=" N LEU A 507 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N CYS A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Proline residue: A 509 - end of helix removed outlier: 3.635A pdb=" N PHE A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N SER A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 756 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: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 976 1.34 - 1.46: 554 1.46 - 1.57: 1738 1.57 - 1.69: 1 1.69 - 1.80: 26 Bond restraints: 3295 Sorted by residual: bond pdb=" C11 S1P A 601 " pdb=" C12 S1P A 601 " ideal model delta sigma weight residual 1.573 1.524 0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" C12 S1P A 601 " pdb=" C13 S1P A 601 " ideal model delta sigma weight residual 1.569 1.523 0.046 2.00e-02 2.50e+03 5.25e+00 bond pdb=" C13 S1P A 601 " pdb=" C14 S1P A 601 " ideal model delta sigma weight residual 1.569 1.524 0.045 2.00e-02 2.50e+03 5.13e+00 bond pdb=" C10 S1P A 601 " pdb=" C11 S1P A 601 " ideal model delta sigma weight residual 1.562 1.524 0.038 2.00e-02 2.50e+03 3.58e+00 bond pdb=" C15 S1P A 601 " pdb=" C16 S1P A 601 " ideal model delta sigma weight residual 1.561 1.525 0.036 2.00e-02 2.50e+03 3.32e+00 ... (remaining 3290 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.48: 67 106.48 - 113.36: 1839 113.36 - 120.23: 1301 120.23 - 127.10: 1228 127.10 - 133.97: 34 Bond angle restraints: 4469 Sorted by residual: angle pdb=" C GLY A 333 " pdb=" N MET A 334 " pdb=" CA MET A 334 " ideal model delta sigma weight residual 121.64 115.64 6.00 2.13e+00 2.20e-01 7.92e+00 angle pdb=" N PHE A 176 " pdb=" CA PHE A 176 " pdb=" CB PHE A 176 " ideal model delta sigma weight residual 110.39 114.93 -4.54 1.75e+00 3.27e-01 6.73e+00 angle pdb=" N LYS A 224 " pdb=" CA LYS A 224 " pdb=" C LYS A 224 " ideal model delta sigma weight residual 111.02 114.17 -3.15 1.22e+00 6.72e-01 6.67e+00 angle pdb=" C PHE A 177 " pdb=" N TRP A 178 " pdb=" CA TRP A 178 " ideal model delta sigma weight residual 120.68 116.32 4.36 1.70e+00 3.46e-01 6.58e+00 angle pdb=" N TRP A 178 " pdb=" CA TRP A 178 " pdb=" CB TRP A 178 " ideal model delta sigma weight residual 110.30 114.16 -3.86 1.54e+00 4.22e-01 6.28e+00 ... (remaining 4464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.66: 1700 14.66 - 29.32: 149 29.32 - 43.98: 41 43.98 - 58.64: 10 58.64 - 73.30: 3 Dihedral angle restraints: 1903 sinusoidal: 717 harmonic: 1186 Sorted by residual: dihedral pdb=" CA THR A 223 " pdb=" C THR A 223 " pdb=" N LYS A 224 " pdb=" CA LYS A 224 " ideal model delta harmonic sigma weight residual -180.00 -164.87 -15.13 0 5.00e+00 4.00e-02 9.16e+00 dihedral pdb=" CB MET A 230 " pdb=" CG MET A 230 " pdb=" SD MET A 230 " pdb=" CE MET A 230 " ideal model delta sinusoidal sigma weight residual 180.00 127.67 52.33 3 1.50e+01 4.44e-03 9.10e+00 dihedral pdb=" CA VAL A 252 " pdb=" C VAL A 252 " pdb=" N LYS A 253 " pdb=" CA LYS A 253 " ideal model delta harmonic sigma weight residual 180.00 165.00 15.00 0 5.00e+00 4.00e-02 9.00e+00 ... (remaining 1900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 286 0.029 - 0.059: 171 0.059 - 0.088: 41 0.088 - 0.117: 21 0.117 - 0.147: 6 Chirality restraints: 525 Sorted by residual: chirality pdb=" CA SER A 475 " pdb=" N SER A 475 " pdb=" C SER A 475 " pdb=" CB SER A 475 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CB VAL A 125 " pdb=" CA VAL A 125 " pdb=" CG1 VAL A 125 " pdb=" CG2 VAL A 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA PHE A 176 " pdb=" N PHE A 176 " pdb=" C PHE A 176 " pdb=" CB PHE A 176 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 522 not shown) Planarity restraints: 543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 178 " 0.022 2.00e-02 2.50e+03 1.82e-02 8.28e+00 pdb=" CG TRP A 178 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 178 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 178 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 178 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 178 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 178 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 178 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 178 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 178 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 176 " -0.012 2.00e-02 2.50e+03 1.41e-02 3.46e+00 pdb=" CG PHE A 176 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 176 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 176 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 176 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 176 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 176 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 266 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 267 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 267 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 267 " -0.019 5.00e-02 4.00e+02 ... (remaining 540 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 23 2.65 - 3.21: 3208 3.21 - 3.77: 5165 3.77 - 4.34: 6786 4.34 - 4.90: 11488 Nonbonded interactions: 26670 Sorted by model distance: nonbonded pdb=" OH TYR A 246 " pdb=" O GLY A 333 " model vdw 2.088 2.440 nonbonded pdb=" O GLY A 219 " pdb=" NH1 ARG A 227 " model vdw 2.262 2.520 nonbonded pdb=" O THR A 223 " pdb=" N ARG A 227 " model vdw 2.287 2.520 nonbonded pdb=" OG1 THR A 373 " pdb=" OE1 GLU A 433 " model vdw 2.342 2.440 nonbonded pdb=" OD2 ASP A 128 " pdb=" NZ LYS A 253 " model vdw 2.355 2.520 ... (remaining 26665 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 group one per residue 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: 2.850 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: 11.500 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 13.810 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 : 0.005 0.049 3295 Z= 0.344 Angle : 0.618 6.572 4469 Z= 0.351 Chirality : 0.041 0.147 525 Planarity : 0.004 0.034 543 Dihedral : 12.797 73.301 1143 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: 2.72 (0.43), residues: 410 helix: 1.97 (0.28), residues: 364 sheet: None (None), residues: 0 loop : 0.65 (1.07), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 178 HIS 0.007 0.002 HIS A 341 PHE 0.033 0.002 PHE A 176 TYR 0.011 0.001 TYR A 116 ARG 0.010 0.001 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.355 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1288 time to fit residues: 6.1487 Evaluate side-chains 31 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.0050 chunk 19 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3295 Z= 0.202 Angle : 0.533 7.789 4469 Z= 0.280 Chirality : 0.039 0.141 525 Planarity : 0.004 0.032 543 Dihedral : 7.438 58.899 463 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.19 % Allowed : 5.04 % Favored : 93.77 % 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: 2.88 (0.43), residues: 410 helix: 2.06 (0.28), residues: 366 sheet: None (None), residues: 0 loop : 0.81 (1.13), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 178 HIS 0.005 0.002 HIS A 341 PHE 0.015 0.001 PHE A 151 TYR 0.012 0.001 TYR A 116 ARG 0.005 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.314 Fit side-chains REVERT: A 439 ASN cc_start: 0.8704 (p0) cc_final: 0.8482 (p0) outliers start: 4 outliers final: 3 residues processed: 41 average time/residue: 0.1722 time to fit residues: 8.7028 Evaluate side-chains 39 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3295 Z= 0.241 Angle : 0.538 8.374 4469 Z= 0.280 Chirality : 0.039 0.140 525 Planarity : 0.004 0.031 543 Dihedral : 7.408 56.052 463 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.48 % Allowed : 6.82 % Favored : 91.69 % 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: 2.80 (0.43), residues: 410 helix: 2.00 (0.28), residues: 366 sheet: None (None), residues: 0 loop : 0.93 (1.17), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 178 HIS 0.005 0.001 HIS A 341 PHE 0.012 0.001 PHE A 327 TYR 0.011 0.001 TYR A 116 ARG 0.004 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.350 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 41 average time/residue: 0.1718 time to fit residues: 8.6780 Evaluate side-chains 38 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.0020 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3295 Z= 0.185 Angle : 0.514 8.007 4469 Z= 0.265 Chirality : 0.038 0.136 525 Planarity : 0.004 0.030 543 Dihedral : 7.172 55.421 463 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.19 % Allowed : 9.50 % Favored : 89.32 % 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: 3.01 (0.43), residues: 410 helix: 2.13 (0.28), residues: 366 sheet: None (None), residues: 0 loop : 1.01 (1.17), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 PHE 0.013 0.001 PHE A 151 TYR 0.011 0.001 TYR A 116 ARG 0.004 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.352 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.1705 time to fit residues: 8.0737 Evaluate side-chains 39 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3295 Z= 0.243 Angle : 0.536 8.071 4469 Z= 0.279 Chirality : 0.039 0.139 525 Planarity : 0.004 0.031 543 Dihedral : 7.262 54.445 463 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.78 % Allowed : 10.98 % Favored : 87.24 % 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: 2.88 (0.43), residues: 410 helix: 2.06 (0.28), residues: 365 sheet: None (None), residues: 0 loop : 0.80 (1.18), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 PHE 0.013 0.001 PHE A 151 TYR 0.011 0.001 TYR A 116 ARG 0.003 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.332 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 41 average time/residue: 0.1671 time to fit residues: 8.4979 Evaluate side-chains 42 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 522 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3295 Z= 0.232 Angle : 0.531 8.203 4469 Z= 0.277 Chirality : 0.039 0.139 525 Planarity : 0.004 0.030 543 Dihedral : 7.253 54.224 463 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.19 % Allowed : 12.17 % Favored : 86.65 % 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: 2.84 (0.43), residues: 410 helix: 2.04 (0.28), residues: 365 sheet: None (None), residues: 0 loop : 0.79 (1.19), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 PHE 0.013 0.001 PHE A 151 TYR 0.011 0.001 TYR A 116 ARG 0.004 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.339 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 39 average time/residue: 0.1742 time to fit residues: 8.4327 Evaluate side-chains 41 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 522 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3295 Z= 0.201 Angle : 0.516 8.038 4469 Z= 0.270 Chirality : 0.038 0.136 525 Planarity : 0.004 0.030 543 Dihedral : 7.144 53.933 463 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.48 % Allowed : 12.46 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.43), residues: 410 helix: 2.10 (0.28), residues: 365 sheet: None (None), residues: 0 loop : 0.82 (1.18), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 178 HIS 0.003 0.001 HIS A 341 PHE 0.014 0.001 PHE A 151 TYR 0.011 0.001 TYR A 116 ARG 0.005 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.350 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 40 average time/residue: 0.1915 time to fit residues: 9.2997 Evaluate side-chains 40 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 522 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3295 Z= 0.245 Angle : 0.541 8.589 4469 Z= 0.284 Chirality : 0.039 0.138 525 Planarity : 0.004 0.031 543 Dihedral : 7.258 53.764 463 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.48 % Allowed : 14.24 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.43), residues: 410 helix: 2.04 (0.28), residues: 364 sheet: None (None), residues: 0 loop : 0.59 (1.17), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 PHE 0.026 0.001 PHE A 498 TYR 0.010 0.001 TYR A 116 ARG 0.001 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 393 GLN cc_start: 0.6899 (tt0) cc_final: 0.6579 (tt0) outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 0.1671 time to fit residues: 8.5105 Evaluate side-chains 40 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 522 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.1980 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3295 Z= 0.186 Angle : 0.528 8.676 4469 Z= 0.271 Chirality : 0.038 0.138 525 Planarity : 0.004 0.030 543 Dihedral : 7.073 53.569 463 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.19 % Allowed : 13.65 % Favored : 85.16 % 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: 2.80 (0.44), residues: 410 helix: 2.04 (0.28), residues: 364 sheet: None (None), residues: 0 loop : 0.59 (1.17), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 178 HIS 0.003 0.001 HIS A 341 PHE 0.014 0.001 PHE A 151 TYR 0.011 0.001 TYR A 116 ARG 0.001 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 375 PHE cc_start: 0.7865 (m-10) cc_final: 0.7596 (m-10) outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 0.1438 time to fit residues: 6.8668 Evaluate side-chains 39 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 522 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.0970 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3295 Z= 0.188 Angle : 0.529 8.645 4469 Z= 0.273 Chirality : 0.038 0.136 525 Planarity : 0.004 0.030 543 Dihedral : 7.036 54.563 463 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.19 % Allowed : 13.65 % Favored : 85.16 % 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: 2.80 (0.44), residues: 410 helix: 2.03 (0.28), residues: 364 sheet: None (None), residues: 0 loop : 0.62 (1.16), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 178 HIS 0.003 0.001 HIS A 341 PHE 0.013 0.001 PHE A 151 TYR 0.011 0.001 TYR A 116 ARG 0.001 0.000 ARG A 487 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 375 PHE cc_start: 0.7838 (m-10) cc_final: 0.7590 (m-10) REVERT: A 393 GLN cc_start: 0.6875 (tt0) cc_final: 0.6566 (tt0) outliers start: 4 outliers final: 4 residues processed: 34 average time/residue: 0.1393 time to fit residues: 6.0998 Evaluate side-chains 35 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 522 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 0.0370 chunk 23 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.181179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.161420 restraints weight = 3570.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.164674 restraints weight = 2331.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.166718 restraints weight = 1742.443| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3295 Z= 0.179 Angle : 0.523 9.055 4469 Z= 0.269 Chirality : 0.038 0.136 525 Planarity : 0.004 0.031 543 Dihedral : 6.963 55.339 463 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.19 % Allowed : 13.95 % Favored : 84.87 % 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: 2.84 (0.44), residues: 410 helix: 2.05 (0.28), residues: 364 sheet: None (None), residues: 0 loop : 0.66 (1.16), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 178 HIS 0.003 0.001 HIS A 341 PHE 0.013 0.001 PHE A 151 TYR 0.011 0.001 TYR A 116 ARG 0.001 0.000 ARG A 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1147.94 seconds wall clock time: 21 minutes 31.09 seconds (1291.09 seconds total)