Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 18:10:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7the_25893/08_2023/7the_25893.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7the_25893/08_2023/7the_25893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7the_25893/08_2023/7the_25893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7the_25893/08_2023/7the_25893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7the_25893/08_2023/7the_25893.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7the_25893/08_2023/7the_25893.pdb" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1543 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. 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-1.21rc1-5044/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: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 97} 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: 2.28, per 1000 atoms: 0.69 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: 1.12 Conformation dependent library (CDL) restraints added in 473.5 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: 0.42 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: 0.89 Time building geometry restraints manager: 1.27 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 1.413 1.482 -0.069 2.00e-02 2.50e+03 1.19e+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: 1822 16.95 - 33.89: 139 33.89 - 50.84: 29 50.84 - 67.79: 7 67.79 - 84.73: 4 Dihedral angle restraints: 2001 sinusoidal: 773 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 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 270 0.076 - 0.152: 164 0.152 - 0.228: 49 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 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: 1.310 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: 6.830 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.570 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 0.069 3388 Z= 0.844 Angle : 1.877 9.080 4605 Z= 1.234 Chirality : 0.106 0.379 499 Planarity : 0.015 0.104 594 Dihedral : 13.729 84.731 1205 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 : 0.355 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: 0.2050 time to fit residues: 30.2020 Evaluate side-chains 87 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5098 ------------------------------------------------------------------------------- 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: 0.7576 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 3388 Z= 0.253 Angle : 0.728 6.514 4605 Z= 0.394 Chirality : 0.047 0.167 499 Planarity : 0.005 0.034 594 Dihedral : 6.857 31.104 468 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 3.60 % 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: -1.64 (0.39), residues: 417 helix: -3.40 (0.66), residues: 35 sheet: 0.02 (0.43), residues: 138 loop : -1.42 (0.37), 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 107 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 101 average time/residue: 0.1639 time to fit residues: 19.9257 Evaluate side-chains 100 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.385 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0373 time to fit residues: 1.2167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 10 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 3388 Z= 0.203 Angle : 0.636 6.844 4605 Z= 0.339 Chirality : 0.045 0.160 499 Planarity : 0.005 0.045 594 Dihedral : 6.025 33.037 468 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer Outliers : 2.77 % 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: -1.31 (0.40), residues: 417 helix: -3.13 (0.73), residues: 35 sheet: 0.04 (0.41), residues: 156 loop : -1.13 (0.41), residues: 226 *********************** 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 111 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.1666 time to fit residues: 20.6112 Evaluate side-chains 93 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.385 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0393 time to fit residues: 0.9750 ------------------------------------------------------------------------------- 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: 0.0000 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 3388 Z= 0.220 Angle : 0.648 6.582 4605 Z= 0.342 Chirality : 0.045 0.152 499 Planarity : 0.005 0.045 594 Dihedral : 5.742 28.374 468 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer Outliers : 3.88 % 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 (0.40), residues: 417 helix: -3.11 (0.73), residues: 35 sheet: 0.10 (0.41), residues: 150 loop : -1.04 (0.40), residues: 232 *********************** 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: 14 poor density : 88 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 92 average time/residue: 0.1738 time to fit residues: 19.0525 Evaluate side-chains 92 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0368 time to fit residues: 1.2648 ------------------------------------------------------------------------------- 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: 2.9990 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.0980 chunk 20 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN C 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 3388 Z= 0.216 Angle : 0.627 6.694 4605 Z= 0.333 Chirality : 0.045 0.185 499 Planarity : 0.005 0.047 594 Dihedral : 5.543 27.733 468 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % 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: -1.19 (0.40), residues: 417 helix: -3.13 (0.71), residues: 35 sheet: 0.15 (0.41), residues: 156 loop : -1.05 (0.41), residues: 226 *********************** 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 99 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 92 average time/residue: 0.1789 time to fit residues: 19.5288 Evaluate side-chains 88 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0356 time to fit residues: 0.8138 ------------------------------------------------------------------------------- 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: 0.7980 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 0.0170 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS B 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 3388 Z= 0.189 Angle : 0.627 6.871 4605 Z= 0.327 Chirality : 0.045 0.184 499 Planarity : 0.005 0.046 594 Dihedral : 5.396 27.440 468 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer Outliers : 2.49 % 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: -1.14 (0.41), residues: 417 helix: -2.97 (0.67), residues: 41 sheet: 0.22 (0.41), residues: 155 loop : -1.00 (0.42), residues: 221 *********************** 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 95 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 89 average time/residue: 0.1547 time to fit residues: 16.7923 Evaluate side-chains 87 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0404 time to fit residues: 1.0246 ------------------------------------------------------------------------------- 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: 4.9990 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.0050 chunk 18 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 3388 Z= 0.174 Angle : 0.620 6.930 4605 Z= 0.327 Chirality : 0.045 0.184 499 Planarity : 0.005 0.047 594 Dihedral : 5.206 26.619 468 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 1.66 % 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: -2.96 (0.67), residues: 41 sheet: 0.28 (0.41), residues: 157 loop : -0.83 (0.43), residues: 219 *********************** 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 98 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 93 average time/residue: 0.1627 time to fit residues: 18.3667 Evaluate side-chains 86 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0405 time to fit residues: 0.8319 ------------------------------------------------------------------------------- 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: 5.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 35 optimal weight: 0.0030 chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- 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: 0.7625 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 3388 Z= 0.330 Angle : 0.699 7.400 4605 Z= 0.378 Chirality : 0.047 0.201 499 Planarity : 0.005 0.047 594 Dihedral : 5.936 27.239 468 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer Outliers : 3.60 % 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: -1.21 (0.41), residues: 417 helix: -3.04 (0.66), residues: 41 sheet: 0.29 (0.42), residues: 151 loop : -1.12 (0.43), residues: 225 *********************** 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 97 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 87 average time/residue: 0.1515 time to fit residues: 16.2485 Evaluate side-chains 91 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0380 time to fit residues: 1.2007 ------------------------------------------------------------------------------- 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: 3.9990 chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 3388 Z= 0.229 Angle : 0.670 7.517 4605 Z= 0.357 Chirality : 0.045 0.156 499 Planarity : 0.005 0.051 594 Dihedral : 5.581 27.212 468 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % 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: -1.16 (0.42), residues: 417 helix: -2.88 (0.67), residues: 47 sheet: 0.27 (0.43), residues: 143 loop : -0.96 (0.42), residues: 227 *********************** 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 93 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 90 average time/residue: 0.1361 time to fit residues: 15.2781 Evaluate side-chains 83 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0342 time to fit residues: 0.7518 ------------------------------------------------------------------------------- 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: 2.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 3388 Z= 0.225 Angle : 0.654 6.617 4605 Z= 0.352 Chirality : 0.046 0.155 499 Planarity : 0.005 0.050 594 Dihedral : 5.556 27.137 468 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer Outliers : 1.66 % 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: -1.26 (0.41), residues: 417 helix: -2.90 (0.66), residues: 47 sheet: 0.19 (0.43), residues: 148 loop : -1.05 (0.42), residues: 222 ********************** 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 88 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 83 average time/residue: 0.1422 time to fit residues: 14.6186 Evaluate side-chains 83 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0463 time to fit residues: 0.8761 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 0.0670 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100AGLN C 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.118288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.106685 restraints weight = 8828.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.109483 restraints weight = 4636.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.111309 restraints weight = 2855.200| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 3388 Z= 0.215 Angle : 0.647 6.593 4605 Z= 0.349 Chirality : 0.045 0.154 499 Planarity : 0.005 0.050 594 Dihedral : 5.472 26.475 468 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % 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: -1.34 (0.41), residues: 417 helix: -2.99 (0.64), residues: 47 sheet: 0.09 (0.41), residues: 155 loop : -1.09 (0.43), residues: 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1280.31 seconds wall clock time: 23 minutes 31.11 seconds (1411.11 seconds total)