Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:21:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v27_31638/11_2022/7v27_31638.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v27_31638/11_2022/7v27_31638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v27_31638/11_2022/7v27_31638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v27_31638/11_2022/7v27_31638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v27_31638/11_2022/7v27_31638.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v27_31638/11_2022/7v27_31638.pdb" } resolution = 4.18 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= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "A ASP 84": "OD1" <-> "OD2" 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: 3252 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "B" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 920 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "A" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 782 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "C" 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: 2.39, per 1000 atoms: 0.73 Number of scatterers: 3252 At special positions: 0 Unit cell: (80.542, 58.576, 99.37, 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 16 16.00 O 636 8.00 N 535 7.00 C 2065 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 90 " 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 C 601 " - " ASN C 343 " Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 491.7 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 10 sheets defined 5.5% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.892A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.642A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'B' and resid 88 through 92 Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 357 removed outlier: 3.604A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 379 through 380 removed outlier: 4.202A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 removed outlier: 4.024A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.680A pdb=" N ARG B 5 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.717A pdb=" N VAL B 12 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 114 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B 36 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU B 52 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TRP B 38 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 60 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.717A pdb=" N VAL B 12 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 114 " --> pdb=" O TYR B 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain 'A' and resid 19 through 22 removed outlier: 3.639A pdb=" N SER A 67 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.028A pdb=" N LEU A 48 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLN A 39 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 50 " --> pdb=" O TRP A 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.028A pdb=" N LEU A 48 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLN A 39 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 50 " --> pdb=" O TRP A 37 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR A 88 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A 104 " --> pdb=" O TYR A 88 " (cutoff:3.500A) 72 hydrogen bonds defined for protein. 171 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.82 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1026 1.35 - 1.47: 885 1.47 - 1.59: 1403 1.59 - 1.71: 0 1.71 - 1.83: 19 Bond restraints: 3333 Sorted by residual: bond pdb=" C VAL C 382 " pdb=" N SER C 383 " ideal model delta sigma weight residual 1.330 1.354 -0.024 1.37e-02 5.33e+03 2.96e+00 bond pdb=" N CYS C 391 " pdb=" CA CYS C 391 " ideal model delta sigma weight residual 1.455 1.465 -0.010 1.21e-02 6.83e+03 6.90e-01 bond pdb=" C ALA C 520 " pdb=" N PRO C 521 " ideal model delta sigma weight residual 1.331 1.340 -0.009 1.20e-02 6.94e+03 6.00e-01 bond pdb=" CA CYS C 391 " pdb=" CB CYS C 391 " ideal model delta sigma weight residual 1.533 1.520 0.013 1.72e-02 3.38e+03 5.91e-01 bond pdb=" C LEU C 335 " pdb=" N CYS C 336 " ideal model delta sigma weight residual 1.326 1.334 -0.008 1.12e-02 7.97e+03 5.50e-01 ... (remaining 3328 not shown) Histogram of bond angle deviations from ideal: 100.88 - 107.49: 127 107.49 - 114.10: 1850 114.10 - 120.72: 1245 120.72 - 127.33: 1286 127.33 - 133.94: 36 Bond angle restraints: 4544 Sorted by residual: angle pdb=" N MET A 49 " pdb=" CA MET A 49 " pdb=" C MET A 49 " ideal model delta sigma weight residual 114.04 110.56 3.48 1.24e+00 6.50e-01 7.89e+00 angle pdb=" N CYS C 432 " pdb=" CA CYS C 432 " pdb=" C CYS C 432 " ideal model delta sigma weight residual 107.88 111.39 -3.51 1.41e+00 5.03e-01 6.18e+00 angle pdb=" N SER A 97 " pdb=" CA SER A 97 " pdb=" C SER A 97 " ideal model delta sigma weight residual 108.34 111.47 -3.13 1.31e+00 5.83e-01 5.70e+00 angle pdb=" CA GLY C 504 " pdb=" C GLY C 504 " pdb=" N TYR C 505 " ideal model delta sigma weight residual 118.95 116.79 2.16 1.06e+00 8.90e-01 4.17e+00 angle pdb=" C PHE C 486 " pdb=" N ASN C 487 " pdb=" CA ASN C 487 " ideal model delta sigma weight residual 121.54 125.16 -3.62 1.91e+00 2.74e-01 3.60e+00 ... (remaining 4539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.03: 1752 15.03 - 30.06: 181 30.06 - 45.10: 28 45.10 - 60.13: 6 60.13 - 75.16: 1 Dihedral angle restraints: 1968 sinusoidal: 750 harmonic: 1218 Sorted by residual: dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 53.66 39.34 1 1.00e+01 1.00e-02 2.18e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 97 " pdb=" CB CYS B 97 " ideal model delta sinusoidal sigma weight residual 93.00 123.94 -30.94 1 1.00e+01 1.00e-02 1.37e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual -86.00 -58.76 -27.24 1 1.00e+01 1.00e-02 1.06e+01 ... (remaining 1965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 366 0.038 - 0.075: 102 0.075 - 0.113: 37 0.113 - 0.150: 5 0.150 - 0.188: 1 Chirality restraints: 511 Sorted by residual: chirality pdb=" CB ILE C 410 " pdb=" CA ILE C 410 " pdb=" CG1 ILE C 410 " pdb=" CG2 ILE C 410 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" CB THR C 500 " pdb=" CA THR C 500 " pdb=" OG1 THR C 500 " pdb=" CG2 THR C 500 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA ILE B 39 " pdb=" N ILE B 39 " pdb=" C ILE B 39 " pdb=" CB ILE B 39 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 508 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.016 5.00e-02 4.00e+02 2.43e-02 9.46e-01 pdb=" N PRO C 521 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 45 " -0.015 5.00e-02 4.00e+02 2.26e-02 8.18e-01 pdb=" N PRO A 46 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 46 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 46 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 31 " 0.015 5.00e-02 4.00e+02 2.24e-02 8.03e-01 pdb=" N PRO B 32 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " 0.012 5.00e-02 4.00e+02 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 546 2.76 - 3.30: 3043 3.30 - 3.83: 5332 3.83 - 4.37: 5987 4.37 - 4.90: 10409 Nonbonded interactions: 25317 Sorted by model distance: nonbonded pdb=" OG1 THR C 430 " pdb=" O PHE C 515 " model vdw 2.229 2.440 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.252 2.440 nonbonded pdb=" O ILE B 106 " pdb=" OH TYR A 38 " model vdw 2.272 2.440 nonbonded pdb=" OG SER A 9 " pdb=" O LYS A 105 " model vdw 2.309 2.440 nonbonded pdb=" O ARG C 408 " pdb=" NE2 GLN C 414 " model vdw 2.313 2.520 ... (remaining 25312 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 16 5.16 5 C 2065 2.51 5 N 535 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.000 Extract box with map and model: 10.990 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 13.780 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.002 0.024 3333 Z= 0.130 Angle : 0.528 4.173 4544 Z= 0.304 Chirality : 0.040 0.188 511 Planarity : 0.003 0.024 580 Dihedral : 11.640 75.160 1176 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % 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: -4.40 (0.34), residues: 415 helix: -3.86 (0.99), residues: 13 sheet: -2.42 (0.44), residues: 126 loop : -3.32 (0.29), residues: 276 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.394 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: 112 average time/residue: 0.2128 time to fit residues: 27.4023 Evaluate side-chains 63 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.350 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4522 ------------------------------------------------------------------------------- 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: 0.5980 chunk 31 optimal weight: 0.0470 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 3333 Z= 0.316 Angle : 0.674 8.155 4544 Z= 0.345 Chirality : 0.045 0.191 511 Planarity : 0.004 0.039 580 Dihedral : 4.356 15.174 465 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer Outliers : 0.28 % 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: -3.80 (0.36), residues: 415 helix: -2.25 (1.99), residues: 7 sheet: -2.13 (0.48), residues: 118 loop : -2.90 (0.31), residues: 290 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.1994 time to fit residues: 19.0608 Evaluate side-chains 62 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.0770 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 0.0470 chunk 29 optimal weight: 0.8980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 ASN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 3333 Z= 0.256 Angle : 0.606 9.142 4544 Z= 0.309 Chirality : 0.044 0.189 511 Planarity : 0.004 0.040 580 Dihedral : 4.333 14.274 465 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % 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: -3.56 (0.37), residues: 415 helix: -2.40 (1.75), residues: 7 sheet: -2.15 (0.45), residues: 130 loop : -2.61 (0.32), residues: 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1765 time to fit residues: 17.9426 Evaluate side-chains 61 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5329 ------------------------------------------------------------------------------- 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: 0.4980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.0470 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 HIS A 62 ASN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3333 Z= 0.234 Angle : 0.615 9.964 4544 Z= 0.307 Chirality : 0.044 0.207 511 Planarity : 0.004 0.040 580 Dihedral : 4.277 16.549 465 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer Outliers : 0.28 % 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: -3.33 (0.38), residues: 415 helix: -2.20 (1.74), residues: 7 sheet: -1.90 (0.46), residues: 134 loop : -2.50 (0.33), residues: 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.1824 time to fit residues: 17.7328 Evaluate side-chains 62 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.395 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5189 ------------------------------------------------------------------------------- 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: 0.6980 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 0.0060 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 3333 Z= 0.281 Angle : 0.650 9.092 4544 Z= 0.326 Chirality : 0.044 0.221 511 Planarity : 0.004 0.040 580 Dihedral : 4.588 17.212 465 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.57 % Favored : 88.43 % 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: -3.14 (0.38), residues: 415 helix: -1.56 (1.81), residues: 7 sheet: -1.85 (0.46), residues: 130 loop : -2.34 (0.32), residues: 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1730 time to fit residues: 16.5043 Evaluate side-chains 62 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4822 ------------------------------------------------------------------------------- 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: 0.7980 chunk 9 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.0870 chunk 3 optimal weight: 0.0060 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 overall best weight: 0.2574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 0.038 3333 Z= 0.177 Angle : 0.607 7.293 4544 Z= 0.303 Chirality : 0.045 0.233 511 Planarity : 0.004 0.039 580 Dihedral : 4.263 18.555 465 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % 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: -2.96 (0.38), residues: 415 helix: -0.86 (1.92), residues: 7 sheet: -1.63 (0.48), residues: 128 loop : -2.29 (0.33), residues: 280 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1704 time to fit residues: 16.5293 Evaluate side-chains 63 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.404 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.0040 chunk 15 optimal weight: 0.0270 chunk 23 optimal weight: 0.1980 chunk 11 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.2850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 GLN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 3333 Z= 0.215 Angle : 0.633 8.085 4544 Z= 0.318 Chirality : 0.045 0.248 511 Planarity : 0.006 0.097 580 Dihedral : 4.406 17.253 465 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % 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: -2.83 (0.39), residues: 415 helix: -1.13 (1.43), residues: 13 sheet: -1.73 (0.47), residues: 133 loop : -2.07 (0.34), residues: 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1936 time to fit residues: 17.8549 Evaluate side-chains 61 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.406 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5155 ------------------------------------------------------------------------------- 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: 0.0070 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 35 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.0670 chunk 22 optimal weight: 0.0030 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.1346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 3333 Z= 0.184 Angle : 0.629 6.950 4544 Z= 0.313 Chirality : 0.045 0.261 511 Planarity : 0.004 0.043 580 Dihedral : 4.255 16.084 465 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % 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: -2.55 (0.39), residues: 415 helix: -0.77 (1.52), residues: 13 sheet: -1.41 (0.48), residues: 128 loop : -1.96 (0.34), residues: 274 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1897 time to fit residues: 17.2825 Evaluate side-chains 59 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5151 ------------------------------------------------------------------------------- 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: 0.0000 chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.0570 chunk 18 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 overall best weight: 0.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 3333 Z= 0.200 Angle : 0.622 7.645 4544 Z= 0.310 Chirality : 0.044 0.270 511 Planarity : 0.004 0.041 580 Dihedral : 4.232 15.924 465 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % 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: -2.49 (0.39), residues: 415 helix: 0.42 (2.37), residues: 7 sheet: -1.42 (0.48), residues: 121 loop : -1.92 (0.34), residues: 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1701 time to fit residues: 15.0827 Evaluate side-chains 56 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.326 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4337 ------------------------------------------------------------------------------- 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: 0.5980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 3333 Z= 0.280 Angle : 0.675 8.235 4544 Z= 0.340 Chirality : 0.045 0.291 511 Planarity : 0.004 0.044 580 Dihedral : 4.629 18.567 465 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % 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: -2.43 (0.39), residues: 415 helix: -0.68 (1.50), residues: 13 sheet: -1.60 (0.47), residues: 121 loop : -1.74 (0.35), residues: 281 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1599 time to fit residues: 14.4442 Evaluate side-chains 57 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.332 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4370 ------------------------------------------------------------------------------- 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: 1.9990 chunk 1 optimal weight: 0.0870 chunk 23 optimal weight: 0.0000 chunk 37 optimal weight: 0.0270 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.0000 chunk 15 optimal weight: 0.0370 chunk 40 optimal weight: 0.1980 overall best weight: 0.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C 481 ASN C 501 ASN A 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.086775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.071758 restraints weight = 12129.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.074339 restraints weight = 7253.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.076210 restraints weight = 5023.391| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 3333 Z= 0.175 Angle : 0.656 6.495 4544 Z= 0.325 Chirality : 0.045 0.264 511 Planarity : 0.004 0.045 580 Dihedral : 4.272 18.990 465 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer Outliers : 0.56 % 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: -2.37 (0.39), residues: 415 helix: -1.10 (1.39), residues: 13 sheet: -1.43 (0.49), residues: 118 loop : -1.74 (0.35), residues: 284 =============================================================================== Job complete usr+sys time: 1408.29 seconds wall clock time: 26 minutes 12.45 seconds (1572.45 seconds total)