Starting phenix.real_space_refine on Thu Dec 7 17:28:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/12_2023/8ex6_28652_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/12_2023/8ex6_28652.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/12_2023/8ex6_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_28652/12_2023/8ex6_28652_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/12_2023/8ex6_28652_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/12_2023/8ex6_28652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/12_2023/8ex6_28652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/12_2023/8ex6_28652_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/12_2023/8ex6_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-1.21rc1-5172/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: 2.28, per 1000 atoms: 0.71 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: 1.36 Conformation dependent library (CDL) restraints added in 569.3 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: 2.40 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: 0.97 Time building geometry restraints manager: 1.46 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: 2.170 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: 11.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.630 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.970 ------------------------------------------------------------------------------- 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 : 0.350 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1334 time to fit residues: 6.4098 Evaluate side-chains 31 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4907 ------------------------------------------------------------------------------- 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 : 0.344 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 41 average time/residue: 0.1711 time to fit residues: 8.7064 Evaluate side-chains 39 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0465 time to fit residues: 0.7221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 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: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7863 moved from start: 0.0872 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 : 0.543 8.454 4469 Z= 0.284 Chirality : 0.040 0.141 525 Planarity : 0.004 0.032 543 Dihedral : 7.425 56.083 463 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.89 % Allowed : 7.42 % 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: 2.79 (0.43), residues: 410 helix: 1.98 (0.28), residues: 366 sheet: None (None), residues: 0 loop : 0.97 (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 0.003 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 41 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.340 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 40 average time/residue: 0.1826 time to fit residues: 8.9817 Evaluate side-chains 36 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0651 time to fit residues: 0.5804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 chunk 35 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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: 0.7816 moved from start: 0.1180 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= 0.183 Angle : 0.512 7.942 4469 Z= 0.265 Chirality : 0.038 0.137 525 Planarity : 0.004 0.030 543 Dihedral : 7.175 55.335 463 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.89 % Allowed : 9.50 % Favored : 89.61 % 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 : 1.02 (1.17), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 PHE 0.014 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 39 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.398 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 0.2144 time to fit residues: 9.6723 Evaluate side-chains 35 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0799 time to fit residues: 0.8983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.0970 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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: 0.7828 moved from start: 0.1285 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= 0.204 Angle : 0.516 7.991 4469 Z= 0.268 Chirality : 0.038 0.137 525 Planarity : 0.004 0.030 543 Dihedral : 7.151 54.411 463 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.59 % Allowed : 10.98 % Favored : 88.43 % 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: 2.99 (0.44), residues: 410 helix: 2.14 (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 0.034 0.001 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 38 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.334 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 38 average time/residue: 0.1745 time to fit residues: 8.2222 Evaluate side-chains 37 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.334 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0668 time to fit residues: 0.5783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7844 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3295 Z= 0.222 Angle : 0.530 8.192 4469 Z= 0.278 Chirality : 0.039 0.138 525 Planarity : 0.004 0.030 543 Dihedral : 7.195 53.947 463 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.59 % Allowed : 12.46 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.43), residues: 410 helix: 2.09 (0.28), residues: 365 sheet: None (None), residues: 0 loop : 0.78 (1.19), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 PHE 0.022 0.001 PHE A 498 TYR 0.011 0.001 TYR A 116 ARG 0.005 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 40 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.357 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 38 average time/residue: 0.1785 time to fit residues: 8.4152 Evaluate side-chains 37 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0359 time to fit residues: 0.5798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 33 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7843 moved from start: 0.1343 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= 0.215 Angle : 0.524 8.268 4469 Z= 0.275 Chirality : 0.039 0.137 525 Planarity : 0.004 0.030 543 Dihedral : 7.167 53.757 463 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.30 % Allowed : 13.06 % 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: 2.88 (0.43), residues: 410 helix: 2.07 (0.28), residues: 365 sheet: None (None), residues: 0 loop : 0.78 (1.19), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 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 39 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.349 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.1767 time to fit residues: 8.4922 Evaluate side-chains 37 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.296 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0685 time to fit residues: 0.6086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7846 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3295 Z= 0.220 Angle : 0.528 8.365 4469 Z= 0.278 Chirality : 0.039 0.137 525 Planarity : 0.004 0.030 543 Dihedral : 7.179 53.492 463 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.59 % Allowed : 12.76 % 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: 2.81 (0.44), residues: 410 helix: 2.02 (0.28), residues: 365 sheet: None (None), residues: 0 loop : 0.75 (1.19), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 178 HIS 0.003 0.002 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 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 38 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.368 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 0.1758 time to fit residues: 8.1083 Evaluate side-chains 36 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0352 time to fit residues: 0.5502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.0870 chunk 40 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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: 0.7841 moved from start: 0.1469 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= 0.217 Angle : 0.546 8.565 4469 Z= 0.283 Chirality : 0.039 0.137 525 Planarity : 0.004 0.030 543 Dihedral : 7.165 53.289 463 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 14.24 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.44), residues: 410 helix: 2.00 (0.28), residues: 365 sheet: None (None), residues: 0 loop : 0.76 (1.19), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 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 *********************** 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 36 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.371 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1541 time to fit residues: 7.1687 Evaluate side-chains 36 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.344 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.0070 chunk 6 optimal weight: 0.5980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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: 0.1512 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= 0.210 Angle : 0.544 8.738 4469 Z= 0.281 Chirality : 0.038 0.137 525 Planarity : 0.004 0.030 543 Dihedral : 7.129 53.225 463 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.59 % Allowed : 13.95 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.44), residues: 410 helix: 2.01 (0.28), residues: 364 sheet: None (None), residues: 0 loop : 0.55 (1.17), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 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 ********************** 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 40 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.288 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 38 average time/residue: 0.1543 time to fit residues: 7.4732 Evaluate side-chains 38 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.295 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0318 time to fit residues: 0.5052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.0070 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.0670 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 40 optimal weight: 0.8980 overall best weight: 0.3136 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.182997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.163640 restraints weight = 3559.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.166857 restraints weight = 2288.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.168961 restraints weight = 1703.266| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3295 Z= 0.160 Angle : 0.514 8.752 4469 Z= 0.264 Chirality : 0.037 0.135 525 Planarity : 0.004 0.030 543 Dihedral : 6.900 56.085 463 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.30 % Allowed : 14.84 % 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: 2.94 (0.44), residues: 410 helix: 2.13 (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 0.047 0.002 TRP A 178 HIS 0.002 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: 1135.85 seconds wall clock time: 21 minutes 34.91 seconds (1294.91 seconds total)