Starting phenix.real_space_refine (version: dev) on Mon Apr 4 12:16:11 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9a_24253/04_2022/7n9a_24253.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9a_24253/04_2022/7n9a_24253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9a_24253/04_2022/7n9a_24253.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9a_24253/04_2022/7n9a_24253.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9a_24253/04_2022/7n9a_24253.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9a_24253/04_2022/7n9a_24253.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 2431 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 886 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "E" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1545 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Time building chain proxies: 2.13, per 1000 atoms: 0.88 Number of scatterers: 2431 At special positions: 0 Unit cell: (79.68, 60.59, 79.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 11 16.00 O 460 8.00 N 420 7.00 C 1540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 94 " distance=2.05 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.04 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: 0.96 Conformation dependent library (CDL) restraints added in 347.6 milliseconds 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 5 sheets defined 13.5% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.524A pdb=" N THR A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.580A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 371 removed outlier: 4.099A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 390 removed outlier: 3.817A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 408 removed outlier: 4.382A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 405 through 408' Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.544A pdb=" N SER A 7 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 21 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 67 " --> pdb=" O GLN A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.786A pdb=" N VAL A 113 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 90 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 91 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ARG A 36 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 45 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.786A pdb=" N VAL A 113 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 90 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.597A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 66 hydrogen bonds defined for protein. 171 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: 0.63 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 796 1.34 - 1.47: 657 1.47 - 1.59: 1025 1.59 - 1.71: 0 1.71 - 1.84: 12 Bond restraints: 2490 Sorted by residual: bond pdb=" N PRO E 499 " pdb=" CD PRO E 499 " ideal model delta sigma weight residual 1.473 1.446 0.027 1.40e-02 5.10e+03 3.76e+00 bond pdb=" CB VAL A 2 " pdb=" CG1 VAL A 2 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.78e+00 bond pdb=" CA PRO E 499 " pdb=" CB PRO E 499 " ideal model delta sigma weight residual 1.534 1.558 -0.024 1.49e-02 4.50e+03 2.65e+00 bond pdb=" CG LEU E 518 " pdb=" CD1 LEU E 518 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" CB PHE A 45 " pdb=" CG PHE A 45 " ideal model delta sigma weight residual 1.502 1.467 0.035 2.30e-02 1.89e+03 2.36e+00 ... (remaining 2485 not shown) Histogram of bond angle deviations from ideal: 95.67 - 103.33: 27 103.33 - 110.99: 803 110.99 - 118.65: 1063 118.65 - 126.30: 1455 126.30 - 133.96: 33 Bond angle restraints: 3381 Sorted by residual: angle pdb=" CA PRO E 499 " pdb=" N PRO E 499 " pdb=" CD PRO E 499 " ideal model delta sigma weight residual 112.00 102.71 9.29 1.40e+00 5.10e-01 4.40e+01 angle pdb=" N GLY E 482 " pdb=" CA GLY E 482 " pdb=" C GLY E 482 " ideal model delta sigma weight residual 114.90 122.64 -7.74 1.54e+00 4.22e-01 2.53e+01 angle pdb=" CA CYS A 22 " pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " ideal model delta sigma weight residual 114.40 125.79 -11.39 2.30e+00 1.89e-01 2.45e+01 angle pdb=" C GLN E 409 " pdb=" N ILE E 410 " pdb=" CA ILE E 410 " ideal model delta sigma weight residual 123.11 117.10 6.01 1.36e+00 5.41e-01 1.95e+01 angle pdb=" CA TYR E 495 " pdb=" CB TYR E 495 " pdb=" CG TYR E 495 " ideal model delta sigma weight residual 113.90 121.76 -7.86 1.80e+00 3.09e-01 1.91e+01 ... (remaining 3376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 1342 16.68 - 33.36: 93 33.36 - 50.04: 20 50.04 - 66.72: 5 66.72 - 83.40: 4 Dihedral angle restraints: 1464 sinusoidal: 569 harmonic: 895 Sorted by residual: dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 94 " pdb=" CB CYS A 94 " ideal model delta sinusoidal sigma weight residual 93.00 165.21 -72.21 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 145.12 -52.12 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" SG CYS E 391 " pdb=" CB CYS E 525 " pdb=" SG CYS E 525 " pdb=" CA CYS E 525 " ideal model delta sinusoidal sigma weight residual -73.00 -14.99 -58.01 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 1461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 202 0.045 - 0.090: 101 0.090 - 0.136: 39 0.136 - 0.181: 12 0.181 - 0.226: 4 Chirality restraints: 358 Sorted by residual: chirality pdb=" CA ASN E 481 " pdb=" N ASN E 481 " pdb=" C ASN E 481 " pdb=" CB ASN E 481 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA PHE E 497 " pdb=" N PHE E 497 " pdb=" C PHE E 497 " pdb=" CB PHE E 497 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CG LEU E 455 " pdb=" CB LEU E 455 " pdb=" CD1 LEU E 455 " pdb=" CD2 LEU E 455 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.65e-01 ... (remaining 355 not shown) Planarity restraints: 445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 498 " 0.067 5.00e-02 4.00e+02 9.57e-02 1.46e+01 pdb=" N PRO E 499 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO E 499 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO E 499 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 495 " -0.026 2.00e-02 2.50e+03 2.25e-02 1.01e+01 pdb=" CG TYR E 495 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR E 495 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR E 495 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR E 495 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR E 495 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR E 495 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 495 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 497 " 0.003 2.00e-02 2.50e+03 2.34e-02 9.60e+00 pdb=" CG PHE E 497 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE E 497 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE E 497 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE E 497 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 PHE E 497 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE E 497 " 0.000 2.00e-02 2.50e+03 ... (remaining 442 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 75 2.69 - 3.24: 2344 3.24 - 3.79: 3625 3.79 - 4.35: 4704 4.35 - 4.90: 7651 Nonbonded interactions: 18399 Sorted by model distance: nonbonded pdb=" O THR A 101 " pdb=" OH TYR E 489 " model vdw 2.135 2.440 nonbonded pdb=" OD1 ASN E 448 " pdb=" ND2 ASN E 450 " model vdw 2.182 2.520 nonbonded pdb=" O GLN E 414 " pdb=" NZ LYS E 424 " model vdw 2.246 2.520 nonbonded pdb=" O ASN A 72 " pdb=" ND2 ASN A 72 " model vdw 2.315 2.520 nonbonded pdb=" OD1 ASN E 388 " pdb=" N ASP E 389 " model vdw 2.316 2.520 ... (remaining 18394 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 11 5.16 5 C 1540 2.51 5 N 420 2.21 5 O 460 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 5.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 25.490 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.070 Process input model: 14.880 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 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 : 0.007 0.055 2490 Z= 0.446 Angle : 1.259 11.386 3381 Z= 0.734 Chirality : 0.064 0.226 358 Planarity : 0.007 0.096 445 Dihedral : 12.628 83.395 885 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.45), residues: 308 helix: -2.13 (0.71), residues: 30 sheet: 1.69 (0.55), residues: 74 loop : -0.48 (0.41), residues: 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.412 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1064 time to fit residues: 9.6521 Evaluate side-chains 67 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.0970 chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.0870 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.2980 chunk 17 optimal weight: 0.4980 chunk 27 optimal weight: 0.1980 chunk 8 optimal weight: 0.0970 overall best weight: 0.1554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 2490 Z= 0.235 Angle : 0.670 6.934 3381 Z= 0.370 Chirality : 0.047 0.135 358 Planarity : 0.007 0.079 445 Dihedral : 5.415 23.315 349 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 3.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.45), residues: 308 helix: -1.84 (0.90), residues: 23 sheet: 1.56 (0.56), residues: 79 loop : -0.59 (0.40), residues: 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.271 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 58 average time/residue: 0.1149 time to fit residues: 8.3054 Evaluate side-chains 58 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.272 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0917 time to fit residues: 0.8291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 14 optimal weight: 0.0050 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 2490 Z= 0.268 Angle : 0.618 6.442 3381 Z= 0.340 Chirality : 0.046 0.145 358 Planarity : 0.006 0.071 445 Dihedral : 5.432 18.633 349 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.45), residues: 308 helix: -2.58 (0.72), residues: 29 sheet: 1.07 (0.55), residues: 79 loop : -0.55 (0.42), residues: 200 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.259 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 67 average time/residue: 0.1235 time to fit residues: 10.0775 Evaluate side-chains 67 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.287 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0289 time to fit residues: 0.6208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 0.0040 chunk 27 optimal weight: 0.7980 chunk 28 optimal weight: 0.0770 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 overall best weight: 0.2750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 2490 Z= 0.284 Angle : 0.643 10.050 3381 Z= 0.342 Chirality : 0.047 0.167 358 Planarity : 0.006 0.065 445 Dihedral : 5.438 17.882 349 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 4.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.44), residues: 308 helix: -2.66 (0.77), residues: 29 sheet: 0.77 (0.55), residues: 79 loop : -0.56 (0.41), residues: 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.277 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 70 average time/residue: 0.1136 time to fit residues: 9.7549 Evaluate side-chains 74 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.280 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0700 time to fit residues: 1.0363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.0060 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 5 optimal weight: 0.0870 chunk 17 optimal weight: 0.7980 overall best weight: 0.1572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 2490 Z= 0.202 Angle : 0.601 7.145 3381 Z= 0.319 Chirality : 0.045 0.141 358 Planarity : 0.004 0.044 445 Dihedral : 5.167 17.736 349 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.44), residues: 308 helix: -2.84 (0.75), residues: 31 sheet: 0.57 (0.55), residues: 79 loop : -0.50 (0.41), residues: 198 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.274 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 65 average time/residue: 0.1238 time to fit residues: 9.8422 Evaluate side-chains 70 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.286 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0341 time to fit residues: 0.6437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 0.0870 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 16 optimal weight: 0.0980 chunk 21 optimal weight: 0.0970 overall best weight: 0.2156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 2490 Z= 0.233 Angle : 0.587 5.298 3381 Z= 0.314 Chirality : 0.045 0.147 358 Planarity : 0.005 0.047 445 Dihedral : 5.166 18.724 349 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.44), residues: 308 helix: -2.91 (0.73), residues: 31 sheet: 0.43 (0.54), residues: 79 loop : -0.64 (0.41), residues: 198 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.266 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 68 average time/residue: 0.1118 time to fit residues: 9.4215 Evaluate side-chains 69 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.264 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1259 time to fit residues: 0.8060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 28 optimal weight: 0.0970 chunk 18 optimal weight: 0.0970 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.0870 chunk 11 optimal weight: 0.0270 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 14 optimal weight: 0.5980 overall best weight: 0.1012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 2490 Z= 0.170 Angle : 0.575 7.699 3381 Z= 0.301 Chirality : 0.044 0.144 358 Planarity : 0.004 0.047 445 Dihedral : 4.751 17.007 349 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.44), residues: 308 helix: -2.80 (0.74), residues: 31 sheet: 0.54 (0.56), residues: 79 loop : -0.62 (0.41), residues: 198 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.309 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 70 average time/residue: 0.1187 time to fit residues: 10.2048 Evaluate side-chains 73 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.272 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0319 time to fit residues: 0.6265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 25 optimal weight: 0.0770 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 21 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 chunk 17 optimal weight: 0.2980 overall best weight: 0.2338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 2490 Z= 0.255 Angle : 0.615 7.097 3381 Z= 0.324 Chirality : 0.045 0.150 358 Planarity : 0.005 0.052 445 Dihedral : 5.000 17.264 349 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.45), residues: 308 helix: -2.78 (0.76), residues: 31 sheet: 0.52 (0.56), residues: 79 loop : -0.77 (0.41), residues: 198 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.248 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 0.1095 time to fit residues: 9.8033 Evaluate side-chains 72 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.257 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0361 time to fit residues: 0.6526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 0.1980 chunk 19 optimal weight: 0.4980 chunk 29 optimal weight: 0.0670 chunk 27 optimal weight: 0.0970 chunk 23 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 14 optimal weight: 0.2980 chunk 25 optimal weight: 0.0470 overall best weight: 0.1214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 ASN E 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 2490 Z= 0.189 Angle : 0.626 7.754 3381 Z= 0.318 Chirality : 0.044 0.140 358 Planarity : 0.005 0.048 445 Dihedral : 4.826 18.073 349 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.44), residues: 308 helix: -2.95 (0.70), residues: 31 sheet: 0.27 (0.56), residues: 81 loop : -0.77 (0.41), residues: 196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.251 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 70 average time/residue: 0.1190 time to fit residues: 10.1985 Evaluate side-chains 71 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.314 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3105 time to fit residues: 1.0474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 chunk 3 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 4 optimal weight: 0.0970 chunk 20 optimal weight: 0.2980 chunk 1 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 overall best weight: 0.2378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 2490 Z= 0.257 Angle : 0.655 7.583 3381 Z= 0.339 Chirality : 0.046 0.146 358 Planarity : 0.005 0.051 445 Dihedral : 5.037 18.381 349 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.44), residues: 308 helix: -2.93 (0.72), residues: 31 sheet: 0.27 (0.55), residues: 81 loop : -0.88 (0.42), residues: 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.263 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 67 average time/residue: 0.1265 time to fit residues: 10.2587 Evaluate side-chains 68 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.285 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0296 time to fit residues: 0.4665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.5980 chunk 16 optimal weight: 0.0470 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 18 optimal weight: 0.0030 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.0470 chunk 29 optimal weight: 0.0770 chunk 1 optimal weight: 0.3980 chunk 28 optimal weight: 0.3980 overall best weight: 0.0544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** 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 = 0.3952 r_free = 0.3952 target = 0.146846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.134292 restraints weight = 4286.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.138243 restraints weight = 2297.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.140830 restraints weight = 1364.858| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 2490 Z= 0.162 Angle : 0.613 7.685 3381 Z= 0.311 Chirality : 0.044 0.141 358 Planarity : 0.005 0.050 445 Dihedral : 4.549 18.594 349 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.45), residues: 308 helix: -2.89 (0.75), residues: 31 sheet: 0.46 (0.57), residues: 80 loop : -0.77 (0.42), residues: 197 =============================================================================== Job complete usr+sys time: 1441.20 seconds wall clock time: 26 minutes 17.21 seconds (1577.21 seconds total)