Starting phenix.real_space_refine (version: dev) on Thu May 12 15:14:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7the_25893/05_2022/7the_25893.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7the_25893/05_2022/7the_25893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7the_25893/05_2022/7the_25893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7the_25893/05_2022/7the_25893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7the_25893/05_2022/7the_25893.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7the_25893/05_2022/7the_25893.pdb" } resolution = 3.79 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= -0.002 sd= 0.031 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 "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 3305 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "B" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "C" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 97, 'PCIS': 2} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.37, per 1000 atoms: 0.72 Number of scatterers: 3305 At special positions: 0 Unit cell: (65.596, 81.466, 87.814, 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 17 16.00 O 641 8.00 N 549 7.00 C 2098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.01 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 539.3 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 778 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 12.5% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.981A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.706A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.854A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'C' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 334 through 335 removed outlier: 7.513A pdb=" N ASN A 334 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.975A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.378A pdb=" N GLU B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE B 34 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.378A pdb=" N GLU B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL B 102 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.730A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) 109 hydrogen bonds defined for protein. 252 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: 0.84 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 928 1.33 - 1.45: 657 1.45 - 1.57: 1781 1.57 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 3388 Sorted by residual: bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.435 1.482 -0.047 1.10e-02 8.26e+03 1.82e+01 bond pdb=" CZ ARG B 94 " pdb=" NH2 ARG B 94 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.10e+01 bond pdb=" CZ ARG A 509 " pdb=" NH2 ARG A 509 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.04e+01 bond pdb=" CZ ARG A 457 " pdb=" NH2 ARG A 457 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.02e+01 bond pdb=" CZ ARG A 357 " pdb=" NH2 ARG A 357 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.02e+01 ... (remaining 3383 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.54: 88 105.54 - 112.83: 1438 112.83 - 120.11: 1594 120.11 - 127.40: 1445 127.40 - 134.68: 40 Bond angle restraints: 4605 Sorted by residual: angle pdb=" CA PHE A 347 " pdb=" CB PHE A 347 " pdb=" CG PHE A 347 " ideal model delta sigma weight residual 113.80 119.35 -5.55 1.00e+00 1.00e+00 3.08e+01 angle pdb=" N CYS A 361 " pdb=" CA CYS A 361 " pdb=" C CYS A 361 " ideal model delta sigma weight residual 108.79 117.19 -8.40 1.53e+00 4.27e-01 3.01e+01 angle pdb=" C THR A 393 " pdb=" N ASN A 394 " pdb=" CA ASN A 394 " ideal model delta sigma weight residual 121.75 130.83 -9.08 1.73e+00 3.34e-01 2.75e+01 angle pdb=" CA ASP A 405 " pdb=" CB ASP A 405 " pdb=" CG ASP A 405 " ideal model delta sigma weight residual 112.60 117.25 -4.65 1.00e+00 1.00e+00 2.16e+01 angle pdb=" CA ASP C 70 " pdb=" CB ASP C 70 " pdb=" CG ASP C 70 " ideal model delta sigma weight residual 112.60 117.16 -4.56 1.00e+00 1.00e+00 2.08e+01 ... (remaining 4600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 1828 16.95 - 33.89: 139 33.89 - 50.84: 29 50.84 - 67.79: 7 67.79 - 84.73: 4 Dihedral angle restraints: 2007 sinusoidal: 779 harmonic: 1228 Sorted by residual: dihedral pdb=" CA ARG B 83 " pdb=" C ARG B 83 " pdb=" N SER B 84 " pdb=" CA SER B 84 " ideal model delta harmonic sigma weight residual 180.00 151.24 28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA TYR B 32 " pdb=" C TYR B 32 " pdb=" N ALA B 33 " pdb=" CA ALA B 33 " ideal model delta harmonic sigma weight residual 180.00 151.82 28.18 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA TYR B 91 " pdb=" C TYR B 91 " pdb=" N CYS B 92 " pdb=" CA CYS B 92 " ideal model delta harmonic sigma weight residual 180.00 152.36 27.64 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 2004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 270 0.076 - 0.152: 165 0.152 - 0.228: 48 0.228 - 0.303: 10 0.303 - 0.379: 6 Chirality restraints: 499 Sorted by residual: chirality pdb=" CA ALA A 520 " pdb=" N ALA A 520 " pdb=" C ALA A 520 " pdb=" CB ALA A 520 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CA ARG B 83 " pdb=" N ARG B 83 " pdb=" C ARG B 83 " pdb=" CB ARG B 83 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA LEU A 455 " pdb=" N LEU A 455 " pdb=" C LEU A 455 " pdb=" CB LEU A 455 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 496 not shown) Planarity restraints: 595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 47 " -0.113 2.00e-02 2.50e+03 5.99e-02 8.96e+01 pdb=" CG TRP B 47 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP B 47 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 47 " 0.069 2.00e-02 2.50e+03 pdb=" NE1 TRP B 47 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TRP B 47 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 47 " 0.087 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 47 " -0.061 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 47 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 47 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 103 " 0.104 2.00e-02 2.50e+03 5.15e-02 6.64e+01 pdb=" CG TRP B 103 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP B 103 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP B 103 " -0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP B 103 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP B 103 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 103 " -0.070 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 103 " 0.056 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 103 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP B 103 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 351 " 0.102 2.00e-02 2.50e+03 5.49e-02 6.03e+01 pdb=" CG TYR A 351 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 351 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR A 351 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR A 351 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 351 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR A 351 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 351 " 0.085 2.00e-02 2.50e+03 ... (remaining 592 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 1818 3.02 - 3.49: 3232 3.49 - 3.96: 5382 3.96 - 4.43: 5919 4.43 - 4.90: 9826 Nonbonded interactions: 26177 Sorted by model distance: nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.548 2.440 nonbonded pdb=" OD1 ASP A 467 " pdb=" OG SER A 469 " model vdw 2.565 2.440 nonbonded pdb=" OE2 GLU A 484 " pdb=" OH TYR B 95 " model vdw 2.566 2.440 nonbonded pdb=" OH TYR B 100B" pdb=" OD1 ASN C 34 " model vdw 2.569 2.440 nonbonded pdb=" OE2 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.588 2.440 ... (remaining 26172 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 17 5.16 5 C 2098 2.51 5 N 549 2.21 5 O 641 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: 0.010 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 6.860 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.030 Process input model: 13.940 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 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 : 0.013 0.047 3388 Z= 0.839 Angle : 1.877 9.080 4605 Z= 1.235 Chirality : 0.106 0.379 499 Planarity : 0.015 0.104 594 Dihedral : 13.703 84.731 1211 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.39), residues: 417 helix: -4.02 (0.48), residues: 40 sheet: 0.21 (0.50), residues: 117 loop : -1.70 (0.35), residues: 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1973 time to fit residues: 29.2482 Evaluate side-chains 87 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.393 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN B 58 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 3388 Z= 0.255 Angle : 0.718 6.122 4605 Z= 0.391 Chirality : 0.047 0.166 499 Planarity : 0.006 0.074 594 Dihedral : 6.794 31.177 474 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.66 (0.38), residues: 417 helix: -3.38 (0.67), residues: 35 sheet: 0.02 (0.43), residues: 138 loop : -1.44 (0.36), residues: 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 11 residues processed: 99 average time/residue: 0.1559 time to fit residues: 18.6157 Evaluate side-chains 100 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.343 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0360 time to fit residues: 1.1311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.0770 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.0980 chunk 10 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.0870 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.1716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 105 GLN C 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 3388 Z= 0.165 Angle : 0.619 7.324 4605 Z= 0.329 Chirality : 0.044 0.164 499 Planarity : 0.006 0.075 594 Dihedral : 5.714 32.445 474 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.14 (0.40), residues: 417 helix: -3.21 (0.71), residues: 35 sheet: 0.12 (0.42), residues: 150 loop : -0.92 (0.40), residues: 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 108 average time/residue: 0.1594 time to fit residues: 20.6515 Evaluate side-chains 90 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.350 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0364 time to fit residues: 0.8276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.0370 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 0.0970 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 3388 Z= 0.206 Angle : 0.629 6.493 4605 Z= 0.335 Chirality : 0.044 0.156 499 Planarity : 0.006 0.072 594 Dihedral : 5.536 28.572 474 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.41), residues: 417 helix: -3.18 (0.73), residues: 35 sheet: 0.26 (0.43), residues: 146 loop : -0.81 (0.40), residues: 236 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 96 average time/residue: 0.1663 time to fit residues: 19.1707 Evaluate side-chains 93 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.402 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0389 time to fit residues: 1.1282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN C 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3388 Z= 0.207 Angle : 0.610 5.907 4605 Z= 0.325 Chirality : 0.044 0.174 499 Planarity : 0.005 0.047 594 Dihedral : 5.394 26.306 474 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.41), residues: 417 helix: -3.04 (0.68), residues: 41 sheet: 0.39 (0.41), residues: 154 loop : -0.97 (0.41), residues: 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 94 average time/residue: 0.1710 time to fit residues: 19.1941 Evaluate side-chains 89 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.394 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0319 time to fit residues: 0.8083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 18 optimal weight: 0.4980 chunk 3 optimal weight: 0.0270 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.0270 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 3388 Z= 0.158 Angle : 0.615 5.984 4605 Z= 0.322 Chirality : 0.045 0.182 499 Planarity : 0.005 0.035 594 Dihedral : 5.060 25.621 474 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.89 (0.41), residues: 417 helix: -3.01 (0.68), residues: 41 sheet: 0.49 (0.43), residues: 147 loop : -0.82 (0.42), residues: 229 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 95 average time/residue: 0.1484 time to fit residues: 17.1519 Evaluate side-chains 91 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0403 time to fit residues: 1.1328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 18 optimal weight: 0.0040 chunk 15 optimal weight: 0.0980 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3388 Z= 0.172 Angle : 0.619 6.247 4605 Z= 0.324 Chirality : 0.045 0.163 499 Planarity : 0.005 0.033 594 Dihedral : 4.951 23.757 474 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.41), residues: 417 helix: -3.32 (0.68), residues: 35 sheet: 0.26 (0.43), residues: 146 loop : -0.69 (0.41), residues: 236 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 96 average time/residue: 0.1583 time to fit residues: 18.4084 Evaluate side-chains 87 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.395 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0453 time to fit residues: 0.7454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 3388 Z= 0.248 Angle : 0.648 8.018 4605 Z= 0.347 Chirality : 0.046 0.226 499 Planarity : 0.005 0.034 594 Dihedral : 5.313 24.287 474 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.00 (0.41), residues: 417 helix: -3.22 (0.58), residues: 48 sheet: 0.25 (0.44), residues: 137 loop : -0.60 (0.41), residues: 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 85 average time/residue: 0.1345 time to fit residues: 14.3362 Evaluate side-chains 89 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.345 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0365 time to fit residues: 1.0220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 3388 Z= 0.234 Angle : 0.657 8.331 4605 Z= 0.349 Chirality : 0.046 0.198 499 Planarity : 0.005 0.036 594 Dihedral : 5.358 25.730 474 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.41), residues: 417 helix: -3.12 (0.61), residues: 48 sheet: 0.25 (0.44), residues: 143 loop : -0.75 (0.41), residues: 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 83 average time/residue: 0.1296 time to fit residues: 13.7039 Evaluate side-chains 80 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.404 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0356 time to fit residues: 0.6546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.0670 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 0.0980 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 3388 Z= 0.191 Angle : 0.651 7.982 4605 Z= 0.345 Chirality : 0.045 0.157 499 Planarity : 0.005 0.035 594 Dihedral : 5.217 25.604 474 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.06 (0.41), residues: 417 helix: -2.92 (0.67), residues: 47 sheet: 0.24 (0.44), residues: 143 loop : -0.79 (0.41), residues: 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 87 average time/residue: 0.1251 time to fit residues: 13.8122 Evaluate side-chains 88 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0452 time to fit residues: 0.9817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.119892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.108623 restraints weight = 8799.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.111475 restraints weight = 4375.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.113245 restraints weight = 2609.247| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 3388 Z= 0.248 Angle : 0.689 6.841 4605 Z= 0.369 Chirality : 0.048 0.304 499 Planarity : 0.005 0.038 594 Dihedral : 5.438 25.669 474 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.23 (0.41), residues: 417 helix: -2.91 (0.67), residues: 47 sheet: 0.16 (0.44), residues: 143 loop : -0.95 (0.41), residues: 227 =============================================================================== Job complete usr+sys time: 1258.54 seconds wall clock time: 23 minutes 14.52 seconds (1394.52 seconds total)