Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 19:06:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/10_2023/8ex6_28652_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/10_2023/8ex6_28652.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/10_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_28652/10_2023/8ex6_28652_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/10_2023/8ex6_28652_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/10_2023/8ex6_28652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/10_2023/8ex6_28652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/10_2023/8ex6_28652_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ex6_28652/10_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-1.21rc1-5097/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: 2.18, per 1000 atoms: 0.68 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: 1.33 Conformation dependent library (CDL) restraints added in 486.9 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: 0.55 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: 0.85 Time building geometry restraints manager: 1.42 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: 147 29.32 - 43.98: 41 43.98 - 58.64: 10 58.64 - 73.30: 2 Dihedral angle restraints: 1900 sinusoidal: 714 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 1897 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: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.420 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.660 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.350 ------------------------------------------------------------------------------- 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 : 12.643 73.301 1140 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 *********************** 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 : 0.342 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1276 time to fit residues: 6.1207 Evaluate side-chains 31 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4844 ------------------------------------------------------------------------------- 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: 0.7827 moved from start: 0.0720 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 : 0.534 7.684 4469 Z= 0.281 Chirality : 0.039 0.141 525 Planarity : 0.004 0.032 543 Dihedral : 6.759 52.482 460 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.19 % Allowed : 5.34 % Favored : 93.47 % 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: 366 sheet: None (None), residues: 0 loop : 0.79 (1.13), residues: 44 *********************** 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 41 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.367 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 39 average time/residue: 0.1712 time to fit residues: 8.3412 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: 0.0439 time to fit residues: 0.6838 ------------------------------------------------------------------------------- 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: 0.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3295 Z= 0.285 Angle : 0.567 8.538 4469 Z= 0.297 Chirality : 0.041 0.143 525 Planarity : 0.004 0.032 543 Dihedral : 6.862 55.658 460 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.19 % Allowed : 6.82 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.43), residues: 410 helix: 1.90 (0.28), residues: 366 sheet: None (None), residues: 0 loop : 0.92 (1.18), residues: 44 *********************** 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 39 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.413 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 38 average time/residue: 0.1785 time to fit residues: 8.4731 Evaluate side-chains 36 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0551 time to fit residues: 0.4813 ------------------------------------------------------------------------------- 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: 1.9990 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7839 moved from start: 0.1015 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= 0.203 Angle : 0.523 7.926 4469 Z= 0.272 Chirality : 0.038 0.138 525 Planarity : 0.004 0.031 543 Dihedral : 6.589 52.345 460 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.30 % Allowed : 9.20 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.43), residues: 410 helix: 2.06 (0.28), residues: 366 sheet: None (None), residues: 0 loop : 0.97 (1.16), residues: 44 *********************** 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: 1 poor density : 39 time to evaluate : 0.340 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.1973 time to fit residues: 9.3379 Evaluate side-chains 37 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.338 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0366 time to fit residues: 0.6251 ------------------------------------------------------------------------------- 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: 0.4980 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7858 moved from start: 0.1162 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= 0.226 Angle : 0.532 8.006 4469 Z= 0.277 Chirality : 0.039 0.139 525 Planarity : 0.004 0.031 543 Dihedral : 6.559 53.290 460 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.89 % Allowed : 10.98 % Favored : 88.13 % 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: 2.87 (0.43), residues: 410 helix: 2.07 (0.28), residues: 365 sheet: None (None), residues: 0 loop : 0.69 (1.17), residues: 45 *********************** 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 39 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.311 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 38 average time/residue: 0.1732 time to fit residues: 8.1734 Evaluate side-chains 37 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.339 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0588 time to fit residues: 0.6403 ------------------------------------------------------------------------------- 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: 0.9990 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 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: 0.7854 moved from start: 0.1257 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= 0.221 Angle : 0.540 8.132 4469 Z= 0.283 Chirality : 0.039 0.137 525 Planarity : 0.004 0.039 543 Dihedral : 6.515 53.368 460 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.30 % Allowed : 11.87 % Favored : 87.83 % 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: 2.82 (0.43), residues: 410 helix: 2.04 (0.28), residues: 365 sheet: None (None), residues: 0 loop : 0.60 (1.17), residues: 45 *********************** 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 39 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.334 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.1771 time to fit residues: 8.3406 Evaluate side-chains 36 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.344 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0356 time to fit residues: 0.5536 ------------------------------------------------------------------------------- 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: 0.0020 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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: 0.1378 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= 0.195 Angle : 0.524 8.250 4469 Z= 0.274 Chirality : 0.039 0.136 525 Planarity : 0.004 0.030 543 Dihedral : 6.387 52.170 460 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: 2.88 (0.43), residues: 410 helix: 2.08 (0.28), residues: 365 sheet: None (None), residues: 0 loop : 0.66 (1.17), residues: 45 *********************** 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 38 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.343 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 38 average time/residue: 0.1826 time to fit residues: 8.5755 Evaluate side-chains 35 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0655 time to fit residues: 0.5783 ------------------------------------------------------------------------------- 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: 0.7980 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.0870 chunk 31 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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: 0.7822 moved from start: 0.1517 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= 0.190 Angle : 0.543 8.621 4469 Z= 0.279 Chirality : 0.038 0.135 525 Planarity : 0.004 0.030 543 Dihedral : 6.316 52.632 460 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.30 % Allowed : 13.35 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.44), residues: 410 helix: 2.14 (0.28), residues: 364 sheet: None (None), residues: 0 loop : 0.33 (1.16), residues: 46 *********************** 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: 1 poor density : 37 time to evaluate : 0.374 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 0.1863 time to fit residues: 8.5209 Evaluate side-chains 37 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0362 time to fit residues: 0.5645 ------------------------------------------------------------------------------- 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: 0.3980 chunk 33 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 38 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.0670 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 overall best weight: 0.3518 ------------------------------------------------------------------------------- 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: 0.7790 moved from start: 0.1676 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= 0.168 Angle : 0.525 8.429 4469 Z= 0.271 Chirality : 0.038 0.135 525 Planarity : 0.004 0.030 543 Dihedral : 6.175 53.838 460 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 14.54 % 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: 3.00 (0.44), residues: 410 helix: 2.18 (0.28), residues: 364 sheet: None (None), residues: 0 loop : 0.50 (1.17), residues: 46 *********************** 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 : 0.341 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1484 time to fit residues: 6.9625 Evaluate side-chains 34 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.320 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4941 ------------------------------------------------------------------------------- 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: 0.9990 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 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: 0.7840 moved from start: 0.1599 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= 0.225 Angle : 0.567 8.787 4469 Z= 0.295 Chirality : 0.040 0.141 525 Planarity : 0.004 0.036 543 Dihedral : 6.355 53.183 460 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 15.73 % 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: 2.82 (0.44), residues: 410 helix: 2.10 (0.28), residues: 364 sheet: None (None), residues: 0 loop : 0.13 (1.18), residues: 46 ********************** 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 38 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.342 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1476 time to fit residues: 7.1911 Evaluate side-chains 38 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4787 ------------------------------------------------------------------------------- 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: 0.5980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.0060 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.179767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.159679 restraints weight = 3592.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.162849 restraints weight = 2365.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.164911 restraints weight = 1778.754| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1618 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= 0.211 Angle : 0.554 8.776 4469 Z= 0.288 Chirality : 0.039 0.138 525 Planarity : 0.004 0.031 543 Dihedral : 6.297 52.330 460 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 15.73 % 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: 2.77 (0.44), residues: 410 helix: 2.06 (0.28), residues: 364 sheet: None (None), residues: 0 loop : 0.16 (1.20), residues: 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1119.10 seconds wall clock time: 20 minutes 51.99 seconds (1251.99 seconds total)