Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:43:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx5_23566/11_2022/7lx5_23566.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx5_23566/11_2022/7lx5_23566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx5_23566/11_2022/7lx5_23566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx5_23566/11_2022/7lx5_23566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx5_23566/11_2022/7lx5_23566.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx5_23566/11_2022/7lx5_23566.pdb" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3485 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1552 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "C" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 982 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "A" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 951 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Time building chain proxies: 2.52, per 1000 atoms: 0.72 Number of scatterers: 3485 At special positions: 0 Unit cell: (61.92, 80.84, 99.76, 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 19 16.00 O 669 8.00 N 591 7.00 C 2206 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 112 " distance=2.02 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " 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 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 549.2 milliseconds 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 802 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 9 sheets defined 14.1% alpha, 47.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.526A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.313A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.330A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.776A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 113 through 117 removed outlier: 3.577A pdb=" N MET C 117 " --> pdb=" O HIS C 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.971A pdb=" N ARG A 31 " --> pdb=" O THR A 28 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 32' Processing helix chain 'A' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 7.537A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER B 375 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE A 110 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 112 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 117 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLY A 10 " --> pdb=" O THR A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 354 through 358 removed outlier: 7.537A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER B 375 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE A 110 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 112 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 92 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N MET A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLY A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.521A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE C 34 " --> pdb=" O CYS C 50 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N SER C 52 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TYR C 32 " --> pdb=" O SER C 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR C 119 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.521A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE C 34 " --> pdb=" O CYS C 50 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N SER C 52 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TYR C 32 " --> pdb=" O SER C 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 102 through 104 Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.584A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 5 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 23 " --> pdb=" O GLN A 5 " (cutoff:3.500A) 159 hydrogen bonds defined for protein. 399 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: 0.98 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1125 1.34 - 1.46: 961 1.46 - 1.58: 1465 1.58 - 1.70: 0 1.70 - 1.81: 24 Bond restraints: 3575 Sorted by residual: bond pdb=" CB VAL B 350 " pdb=" CG1 VAL B 350 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.76e-01 bond pdb=" CB TRP C 120 " pdb=" CG TRP C 120 " ideal model delta sigma weight residual 1.498 1.470 0.028 3.10e-02 1.04e+03 7.91e-01 bond pdb=" CG LEU B 461 " pdb=" CD2 LEU B 461 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.71e-01 bond pdb=" CB TRP C 36 " pdb=" CG TRP C 36 " ideal model delta sigma weight residual 1.498 1.471 0.027 3.10e-02 1.04e+03 7.65e-01 bond pdb=" CB PRO A 106 " pdb=" CG PRO A 106 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.53e-01 ... (remaining 3570 not shown) Histogram of bond angle deviations from ideal: 100.62 - 107.30: 109 107.30 - 113.98: 1883 113.98 - 120.67: 1431 120.67 - 127.35: 1390 127.35 - 134.03: 35 Bond angle restraints: 4848 Sorted by residual: angle pdb=" CA LEU B 461 " pdb=" CB LEU B 461 " pdb=" CG LEU B 461 " ideal model delta sigma weight residual 116.30 125.54 -9.24 3.50e+00 8.16e-02 6.97e+00 angle pdb=" CA ARG A 30 " pdb=" CB ARG A 30 " pdb=" CG ARG A 30 " ideal model delta sigma weight residual 114.10 108.92 5.18 2.00e+00 2.50e-01 6.70e+00 angle pdb=" N GLY B 485 " pdb=" CA GLY B 485 " pdb=" C GLY B 485 " ideal model delta sigma weight residual 113.18 108.49 4.69 2.37e+00 1.78e-01 3.92e+00 angle pdb=" C ARG A 30 " pdb=" N ARG A 31 " pdb=" CA ARG A 31 " ideal model delta sigma weight residual 123.24 120.36 2.88 1.54e+00 4.22e-01 3.49e+00 angle pdb=" N GLY A 15 " pdb=" CA GLY A 15 " pdb=" C GLY A 15 " ideal model delta sigma weight residual 115.36 112.93 2.43 1.33e+00 5.65e-01 3.34e+00 ... (remaining 4843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 1968 16.02 - 32.04: 101 32.04 - 48.06: 16 48.06 - 64.07: 2 64.07 - 80.09: 3 Dihedral angle restraints: 2090 sinusoidal: 810 harmonic: 1280 Sorted by residual: dihedral pdb=" CA SER B 366 " pdb=" C SER B 366 " pdb=" N VAL B 367 " pdb=" CA VAL B 367 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA TYR B 489 " pdb=" C TYR B 489 " pdb=" N PHE B 490 " pdb=" CA PHE B 490 " ideal model delta harmonic sigma weight residual 180.00 163.15 16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB GLU B 471 " pdb=" CG GLU B 471 " pdb=" CD GLU B 471 " pdb=" OE1 GLU B 471 " ideal model delta sinusoidal sigma weight residual 0.00 80.09 -80.09 1 3.00e+01 1.11e-03 8.83e+00 ... (remaining 2087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 311 0.031 - 0.063: 112 0.063 - 0.094: 48 0.094 - 0.126: 23 0.126 - 0.157: 7 Chirality restraints: 501 Sorted by residual: chirality pdb=" CG LEU B 461 " pdb=" CB LEU B 461 " pdb=" CD1 LEU B 461 " pdb=" CD2 LEU B 461 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA VAL A 40 " pdb=" N VAL A 40 " pdb=" C VAL A 40 " pdb=" CB VAL A 40 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ARG A 30 " pdb=" N ARG A 30 " pdb=" C ARG A 30 " pdb=" CB ARG A 30 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 498 not shown) Planarity restraints: 633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 110 " -0.010 2.00e-02 2.50e+03 8.62e-03 1.30e+00 pdb=" CG PHE A 110 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 110 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 110 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 110 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 110 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 110 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 80 " 0.007 2.00e-02 2.50e+03 6.42e-03 8.25e-01 pdb=" CG TYR C 80 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR C 80 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 80 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 80 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 80 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 80 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 80 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 467 " -0.004 2.00e-02 2.50e+03 8.40e-03 7.06e-01 pdb=" C ASP B 467 " 0.015 2.00e-02 2.50e+03 pdb=" O ASP B 467 " -0.005 2.00e-02 2.50e+03 pdb=" N ILE B 468 " -0.005 2.00e-02 2.50e+03 ... (remaining 630 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 268 2.74 - 3.28: 3134 3.28 - 3.82: 5333 3.82 - 4.36: 6330 4.36 - 4.90: 11179 Nonbonded interactions: 26244 Sorted by model distance: nonbonded pdb=" OE1 GLN B 498 " pdb=" OG1 THR C 28 " model vdw 2.198 2.440 nonbonded pdb=" OH TYR A 52 " pdb=" O TRP A 105 " model vdw 2.256 2.440 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.258 2.440 nonbonded pdb=" O PHE A 29 " pdb=" NH2 ARG A 71 " model vdw 2.268 2.520 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.292 2.440 ... (remaining 26239 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 19 5.16 5 C 2206 2.51 5 N 591 2.21 5 O 669 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 individual isotropic 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: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.540 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 14.100 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 3575 Z= 0.315 Angle : 0.616 9.238 4848 Z= 0.336 Chirality : 0.045 0.157 501 Planarity : 0.003 0.021 633 Dihedral : 10.099 80.092 1267 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.38), residues: 442 helix: -4.06 (0.60), residues: 27 sheet: 0.79 (0.46), residues: 132 loop : -0.43 (0.35), residues: 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.422 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1929 time to fit residues: 32.3961 Evaluate side-chains 112 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.421 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 0.0010 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 3575 Z= 0.324 Angle : 0.664 9.306 4848 Z= 0.354 Chirality : 0.046 0.185 501 Planarity : 0.004 0.025 633 Dihedral : 4.654 20.247 500 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 5.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.38), residues: 442 helix: -4.25 (0.56), residues: 27 sheet: 1.49 (0.45), residues: 128 loop : -0.58 (0.33), residues: 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.407 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 138 average time/residue: 0.2111 time to fit residues: 33.6912 Evaluate side-chains 132 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 0.416 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0349 time to fit residues: 1.2544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 32 optimal weight: 0.0470 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 1 GLN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3575 Z= 0.173 Angle : 0.586 7.044 4848 Z= 0.306 Chirality : 0.043 0.146 501 Planarity : 0.003 0.025 633 Dihedral : 4.099 15.137 500 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.38), residues: 442 helix: -4.13 (0.57), residues: 28 sheet: 1.86 (0.44), residues: 128 loop : -0.49 (0.34), residues: 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 126 average time/residue: 0.2073 time to fit residues: 30.1846 Evaluate side-chains 117 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0418 time to fit residues: 0.9998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 20 optimal weight: 0.1980 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 3575 Z= 0.208 Angle : 0.607 8.473 4848 Z= 0.311 Chirality : 0.045 0.183 501 Planarity : 0.003 0.025 633 Dihedral : 4.034 16.519 500 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 3.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.38), residues: 442 helix: -3.89 (0.84), residues: 21 sheet: 1.65 (0.42), residues: 128 loop : -0.49 (0.34), residues: 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 120 average time/residue: 0.2154 time to fit residues: 30.0172 Evaluate side-chains 119 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0372 time to fit residues: 1.0874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3575 Z= 0.181 Angle : 0.597 6.974 4848 Z= 0.307 Chirality : 0.043 0.145 501 Planarity : 0.003 0.025 633 Dihedral : 3.852 14.248 500 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.38), residues: 442 helix: -3.60 (0.96), residues: 21 sheet: 1.69 (0.43), residues: 128 loop : -0.40 (0.35), residues: 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 117 average time/residue: 0.2220 time to fit residues: 30.1612 Evaluate side-chains 116 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0484 time to fit residues: 0.9964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 3575 Z= 0.174 Angle : 0.612 10.710 4848 Z= 0.306 Chirality : 0.042 0.145 501 Planarity : 0.003 0.025 633 Dihedral : 3.708 13.642 500 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.39), residues: 442 helix: -3.52 (0.78), residues: 27 sheet: 1.59 (0.43), residues: 137 loop : -0.35 (0.36), residues: 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 120 average time/residue: 0.1955 time to fit residues: 27.2820 Evaluate side-chains 118 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 0.437 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0341 time to fit residues: 0.9358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 3575 Z= 0.170 Angle : 0.582 7.244 4848 Z= 0.296 Chirality : 0.042 0.147 501 Planarity : 0.003 0.026 633 Dihedral : 3.597 12.766 500 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.39), residues: 442 helix: -3.49 (0.68), residues: 34 sheet: 1.95 (0.44), residues: 127 loop : -0.27 (0.36), residues: 281 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 118 average time/residue: 0.2037 time to fit residues: 27.9429 Evaluate side-chains 119 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 0.450 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0474 time to fit residues: 0.7815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 3575 Z= 0.235 Angle : 0.680 12.298 4848 Z= 0.339 Chirality : 0.043 0.146 501 Planarity : 0.004 0.048 633 Dihedral : 4.007 23.043 500 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.40), residues: 442 helix: -3.27 (0.85), residues: 28 sheet: 1.68 (0.43), residues: 136 loop : -0.34 (0.37), residues: 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 119 average time/residue: 0.2156 time to fit residues: 29.7403 Evaluate side-chains 119 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0381 time to fit residues: 0.7602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 3575 Z= 0.299 Angle : 0.668 8.651 4848 Z= 0.346 Chirality : 0.045 0.183 501 Planarity : 0.004 0.026 633 Dihedral : 4.254 16.230 500 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.40), residues: 442 helix: -3.26 (0.89), residues: 28 sheet: 1.59 (0.44), residues: 136 loop : -0.47 (0.36), residues: 278 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 120 average time/residue: 0.1958 time to fit residues: 27.3407 Evaluate side-chains 122 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 0.436 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0445 time to fit residues: 1.0280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 0.0970 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 overall best weight: 1.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 3575 Z= 0.234 Angle : 0.662 10.476 4848 Z= 0.338 Chirality : 0.044 0.162 501 Planarity : 0.003 0.027 633 Dihedral : 4.087 16.616 500 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.39), residues: 442 helix: -3.72 (0.64), residues: 34 sheet: 1.51 (0.43), residues: 136 loop : -0.49 (0.37), residues: 272 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 115 average time/residue: 0.2023 time to fit residues: 27.2578 Evaluate side-chains 115 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 0.424 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0642 time to fit residues: 0.6686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 0.2980 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 0.0010 chunk 26 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.106406 restraints weight = 5771.258| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.63 r_work: 0.3262 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work: 0.3246 rms_B_bonded: 3.42 restraints_weight: 0.1250 r_work: 0.3238 rms_B_bonded: 3.45 restraints_weight: 0.0625 r_work: 0.3229 rms_B_bonded: 3.50 restraints_weight: 0.0312 r_work: 0.3220 rms_B_bonded: 3.57 restraints_weight: 0.0156 r_work: 0.3211 rms_B_bonded: 3.65 restraints_weight: 0.0078 r_work: 0.3201 rms_B_bonded: 3.74 restraints_weight: 0.0039 r_work: 0.3191 rms_B_bonded: 3.85 restraints_weight: 0.0020 r_work: 0.3182 rms_B_bonded: 3.97 restraints_weight: 0.0010 r_work: 0.3172 rms_B_bonded: 4.09 restraints_weight: 0.0005 r_work: 0.3162 rms_B_bonded: 4.23 restraints_weight: 0.0002 r_work: 0.3151 rms_B_bonded: 4.39 restraints_weight: 0.0001 r_work: 0.3140 rms_B_bonded: 4.56 restraints_weight: 0.0001 r_work: 0.3129 rms_B_bonded: 4.74 restraints_weight: 0.0000 r_work: 0.3117 rms_B_bonded: 4.93 restraints_weight: 0.0000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 3575 Z= 0.187 Angle : 0.635 10.385 4848 Z= 0.322 Chirality : 0.043 0.148 501 Planarity : 0.003 0.027 633 Dihedral : 3.817 15.270 500 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.40), residues: 442 helix: -3.69 (0.64), residues: 34 sheet: 1.38 (0.44), residues: 139 loop : -0.42 (0.37), residues: 269 =============================================================================== Job complete usr+sys time: 1312.69 seconds wall clock time: 25 minutes 14.96 seconds (1514.96 seconds total)