Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:08:18 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9a_24253/11_2022/7n9a_24253.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9a_24253/11_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_24253/11_2022/7n9a_24253.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9a_24253/11_2022/7n9a_24253.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9a_24253/11_2022/7n9a_24253.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9a_24253/11_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 Anisotropic ADP refinement not supported. Converting 1545 atoms to isotropic. 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-4778/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: 1.96, per 1000 atoms: 0.81 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: 0.98 Conformation dependent library (CDL) restraints added in 370.1 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: 0.17 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: 0.57 Time building geometry restraints manager: 1.07 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: 4.800 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: 25.610 Check model and map are aligned: 0.030 Convert atoms to be neutral: 0.030 Process input model: 14.820 Find NCS groups from input model: 0.060 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: 48.200 ------------------------------------------------------------------------------- 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 : 0.246 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1127 time to fit residues: 10.2061 Evaluate side-chains 66 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.281 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3808 ------------------------------------------------------------------------------- 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: 0.0980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 17 optimal weight: 0.3980 chunk 27 optimal weight: 0.0470 chunk 8 optimal weight: 0.3980 overall best weight: 0.2076 ------------------------------------------------------------------------------- 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: 0.6969 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 2490 Z= 0.243 Angle : 0.672 6.863 3381 Z= 0.368 Chirality : 0.047 0.135 358 Planarity : 0.005 0.038 445 Dihedral : 5.515 22.259 349 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: -0.36 (0.44), residues: 308 helix: -2.51 (0.70), residues: 31 sheet: 1.54 (0.55), residues: 79 loop : -0.62 (0.40), residues: 198 *********************** 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 67 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.252 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 63 average time/residue: 0.1091 time to fit residues: 8.5584 Evaluate side-chains 63 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.270 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0945 time to fit residues: 0.7950 ------------------------------------------------------------------------------- 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: 0.6980 chunk 7 optimal weight: 0.3980 chunk 27 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 21 optimal weight: 0.4980 chunk 26 optimal weight: 0.4980 chunk 20 optimal weight: 0.0970 chunk 14 optimal weight: 0.5980 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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: 0.7042 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 2490 Z= 0.352 Angle : 0.662 6.289 3381 Z= 0.366 Chirality : 0.048 0.147 358 Planarity : 0.006 0.044 445 Dihedral : 5.765 19.616 349 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % 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: -0.67 (0.45), residues: 308 helix: -2.71 (0.71), residues: 29 sheet: 1.01 (0.55), residues: 79 loop : -0.71 (0.41), 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 72 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.277 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 67 average time/residue: 0.1222 time to fit residues: 10.0305 Evaluate side-chains 73 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.264 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0263 time to fit residues: 0.5278 ------------------------------------------------------------------------------- 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: 0.6980 chunk 13 optimal weight: 0.4980 chunk 18 optimal weight: 0.1980 chunk 27 optimal weight: 0.2980 chunk 28 optimal weight: 0.0670 chunk 14 optimal weight: 0.2980 chunk 25 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.0770 chunk 0 optimal weight: 0.9990 overall best weight: 0.1876 ------------------------------------------------------------------------------- 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: 0.7002 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 2490 Z= 0.217 Angle : 0.617 10.368 3381 Z= 0.324 Chirality : 0.046 0.137 358 Planarity : 0.005 0.044 445 Dihedral : 5.317 18.007 349 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 3.88 % 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: -0.72 (0.44), residues: 308 helix: -2.70 (0.76), residues: 29 sheet: 0.72 (0.56), residues: 79 loop : -0.62 (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 79 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.315 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 72 average time/residue: 0.1023 time to fit residues: 9.2060 Evaluate side-chains 76 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.276 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0681 time to fit residues: 1.0114 ------------------------------------------------------------------------------- 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: 0.4980 chunk 11 optimal weight: 0.0970 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 0.0060 chunk 26 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 overall best weight: 0.2194 ------------------------------------------------------------------------------- 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: 0.7011 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 2490 Z= 0.249 Angle : 0.600 6.864 3381 Z= 0.324 Chirality : 0.045 0.145 358 Planarity : 0.005 0.048 445 Dihedral : 5.316 18.440 349 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % 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: -0.85 (0.44), residues: 308 helix: -2.89 (0.74), residues: 31 sheet: 0.53 (0.55), residues: 79 loop : -0.61 (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 71 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.272 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 63 average time/residue: 0.1238 time to fit residues: 9.4983 Evaluate side-chains 68 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.275 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0328 time to fit residues: 0.6568 ------------------------------------------------------------------------------- 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: 0.0980 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 chunk 16 optimal weight: 0.4980 chunk 21 optimal weight: 0.0970 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: 0.7019 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 2490 Z= 0.246 Angle : 0.591 5.678 3381 Z= 0.319 Chirality : 0.045 0.161 358 Planarity : 0.005 0.047 445 Dihedral : 5.288 18.835 349 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.13 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: -0.98 (0.44), residues: 308 helix: -2.88 (0.76), residues: 31 sheet: 0.52 (0.55), residues: 79 loop : -0.76 (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 72 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.277 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 69 average time/residue: 0.1173 time to fit residues: 10.2330 Evaluate side-chains 67 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1621 time to fit residues: 1.1106 ------------------------------------------------------------------------------- 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: 0.0470 chunk 24 optimal weight: 0.0980 chunk 28 optimal weight: 0.1980 chunk 18 optimal weight: 0.0570 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 11 optimal weight: 0.0070 chunk 8 optimal weight: 0.4980 chunk 5 optimal weight: 0.0070 chunk 19 optimal weight: 0.0980 chunk 14 optimal weight: 0.4980 overall best weight: 0.0432 ------------------------------------------------------------------------------- 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: 0.6945 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 2490 Z= 0.160 Angle : 0.572 6.472 3381 Z= 0.297 Chirality : 0.044 0.141 358 Planarity : 0.005 0.048 445 Dihedral : 4.718 17.153 349 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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: -0.98 (0.44), residues: 308 helix: -3.15 (0.66), residues: 31 sheet: 0.48 (0.55), residues: 79 loop : -0.69 (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 70 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.286 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 65 average time/residue: 0.1107 time to fit residues: 8.9589 Evaluate side-chains 67 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.264 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0292 time to fit residues: 0.5797 ------------------------------------------------------------------------------- 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: 0.6980 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 0.0870 chunk 16 optimal weight: 0.0770 chunk 11 optimal weight: 0.0070 chunk 21 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 0.0670 chunk 17 optimal weight: 0.6980 overall best weight: 0.1472 ------------------------------------------------------------------------------- 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** E 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 2490 Z= 0.194 Angle : 0.597 7.027 3381 Z= 0.312 Chirality : 0.044 0.145 358 Planarity : 0.005 0.049 445 Dihedral : 4.840 19.092 349 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % 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: -1.02 (0.44), residues: 308 helix: -2.99 (0.70), residues: 31 sheet: 0.39 (0.56), residues: 81 loop : -0.74 (0.41), residues: 196 *********************** 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 71 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.274 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 67 average time/residue: 0.1099 time to fit residues: 9.1043 Evaluate side-chains 69 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.285 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0354 time to fit residues: 0.4900 ------------------------------------------------------------------------------- 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: 0.7980 chunk 17 optimal weight: 0.4980 chunk 13 optimal weight: 0.0870 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.1980 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 14 optimal weight: 0.0970 chunk 25 optimal weight: 0.2980 overall best weight: 0.1556 ------------------------------------------------------------------------------- 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: 0.6983 moved from start: 0.3823 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= 0.193 Angle : 0.595 7.218 3381 Z= 0.310 Chirality : 0.044 0.162 358 Planarity : 0.005 0.048 445 Dihedral : 4.829 18.991 349 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % 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: -1.03 (0.44), residues: 308 helix: -2.89 (0.75), residues: 31 sheet: 0.40 (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: 5 poor density : 68 time to evaluate : 0.275 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 69 average time/residue: 0.1253 time to fit residues: 10.4844 Evaluate side-chains 70 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.277 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1250 time to fit residues: 0.8287 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 chunk 6 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.0970 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.0980 chunk 1 optimal weight: 0.0980 chunk 17 optimal weight: 0.6980 overall best weight: 0.1976 ------------------------------------------------------------------------------- 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: 0.7001 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 2490 Z= 0.225 Angle : 0.628 8.679 3381 Z= 0.324 Chirality : 0.045 0.144 358 Planarity : 0.005 0.050 445 Dihedral : 4.932 19.294 349 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % 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: -1.16 (0.44), residues: 308 helix: -2.83 (0.76), residues: 31 sheet: 0.28 (0.55), residues: 81 loop : -0.88 (0.41), 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 68 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.274 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1278 time to fit residues: 10.5892 Evaluate side-chains 68 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.277 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3959 ------------------------------------------------------------------------------- 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: 0.0870 chunk 16 optimal weight: 0.0770 chunk 20 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.0970 chunk 18 optimal weight: 0.0370 chunk 17 optimal weight: 0.0980 chunk 11 optimal weight: 0.0040 chunk 29 optimal weight: 0.0970 chunk 1 optimal weight: 0.2980 chunk 28 optimal weight: 0.0970 overall best weight: 0.0604 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.147728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.135176 restraints weight = 4305.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.139047 restraints weight = 2326.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.141629 restraints weight = 1379.044| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 2490 Z= 0.159 Angle : 0.612 8.985 3381 Z= 0.310 Chirality : 0.044 0.143 358 Planarity : 0.005 0.050 445 Dihedral : 4.625 19.342 349 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.44), residues: 308 helix: -2.80 (0.79), residues: 31 sheet: 0.38 (0.55), residues: 80 loop : -0.84 (0.41), residues: 197 =============================================================================== Job complete usr+sys time: 1454.00 seconds wall clock time: 26 minutes 34.07 seconds (1594.07 seconds total)