Starting phenix.real_space_refine on Mon Nov 13 16:53:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrj_32728/11_2023/7wrj_32728.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrj_32728/11_2023/7wrj_32728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrj_32728/11_2023/7wrj_32728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrj_32728/11_2023/7wrj_32728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrj_32728/11_2023/7wrj_32728.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrj_32728/11_2023/7wrj_32728.pdb" } resolution = 4.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2091 2.51 5 N 557 2.21 5 O 627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 357": "NH1" <-> "NH2" Residue "R ASP 364": "OD1" <-> "OD2" Residue "R PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 398": "OD1" <-> "OD2" Residue "R ASP 405": "OD1" <-> "OD2" Residue "R ASP 427": "OD1" <-> "OD2" Residue "R TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 93": "OD1" <-> "OD2" Residue "B ASP 94": "OD1" <-> "OD2" Residue "B ARG 106": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 3289 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1504 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Chain: "A" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 973 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "B" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 784 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.36, per 1000 atoms: 0.72 Number of scatterers: 3289 At special positions: 0 Unit cell: (73.83, 75.97, 85.6, 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 14 16.00 O 627 8.00 N 557 7.00 C 2091 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN R 343 " Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 583.0 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 9 sheets defined 7.7% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'R' and resid 364 through 368 Processing helix chain 'R' and resid 403 through 407 removed outlier: 3.704A pdb=" N VAL R 407 " --> pdb=" O GLY R 404 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 502 through 506 Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.954A pdb=" N ASP B 83 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU B 84 " --> pdb=" O SER B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 84' Processing sheet with id=AA1, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.628A pdb=" N VAL R 395 " --> pdb=" O ILE R 358 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL R 512 " --> pdb=" O ASP R 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.510A pdb=" N THR A 83 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.589A pdb=" N ALA A 98 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL A 36 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU A 52 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP A 38 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 52 " --> pdb=" O ARG A 60 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 60 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.868A pdb=" N MET A 115 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 10 Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 19 Processing sheet with id=AA8, first strand: chain 'B' and resid 22 through 23 Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 49 removed outlier: 5.736A pdb=" N LEU B 47 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN B 38 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B 90 " --> pdb=" O ASN B 35 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY B 98 " --> pdb=" O ASP B 93 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 174 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: 0.73 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 997 1.33 - 1.46: 912 1.46 - 1.59: 1448 1.59 - 1.72: 1 1.72 - 1.85: 15 Bond restraints: 3373 Sorted by residual: bond pdb=" CB CYS R 336 " pdb=" SG CYS R 336 " ideal model delta sigma weight residual 1.808 1.716 0.092 3.30e-02 9.18e+02 7.73e+00 bond pdb=" CG1 ILE R 418 " pdb=" CD1 ILE R 418 " ideal model delta sigma weight residual 1.513 1.408 0.105 3.90e-02 6.57e+02 7.27e+00 bond pdb=" C PRO R 373 " pdb=" O PRO R 373 " ideal model delta sigma weight residual 1.235 1.206 0.029 1.30e-02 5.92e+03 5.12e+00 bond pdb=" CA CYS R 525 " pdb=" C CYS R 525 " ideal model delta sigma weight residual 1.527 1.548 -0.021 9.80e-03 1.04e+04 4.56e+00 bond pdb=" N LEU R 371 " pdb=" CA LEU R 371 " ideal model delta sigma weight residual 1.464 1.489 -0.025 1.20e-02 6.94e+03 4.33e+00 ... (remaining 3368 not shown) Histogram of bond angle deviations from ideal: 96.66 - 104.11: 60 104.11 - 111.57: 1403 111.57 - 119.02: 1253 119.02 - 126.47: 1811 126.47 - 133.93: 66 Bond angle restraints: 4593 Sorted by residual: angle pdb=" N PRO R 373 " pdb=" CA PRO R 373 " pdb=" CB PRO R 373 " ideal model delta sigma weight residual 103.25 96.66 6.59 1.05e+00 9.07e-01 3.94e+01 angle pdb=" N ASN R 370 " pdb=" CA ASN R 370 " pdb=" C ASN R 370 " ideal model delta sigma weight residual 113.16 106.83 6.33 1.24e+00 6.50e-01 2.61e+01 angle pdb=" C ASP R 364 " pdb=" N TYR R 365 " pdb=" CA TYR R 365 " ideal model delta sigma weight residual 120.28 127.60 -7.32 1.44e+00 4.82e-01 2.58e+01 angle pdb=" C TYR B 50 " pdb=" N HIS B 51 " pdb=" CA HIS B 51 " ideal model delta sigma weight residual 121.54 130.77 -9.23 1.91e+00 2.74e-01 2.33e+01 angle pdb=" CB GLN R 409 " pdb=" CG GLN R 409 " pdb=" CD GLN R 409 " ideal model delta sigma weight residual 112.60 119.86 -7.26 1.70e+00 3.46e-01 1.82e+01 ... (remaining 4588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.56: 1665 14.56 - 29.12: 241 29.12 - 43.68: 52 43.68 - 58.24: 10 58.24 - 72.80: 5 Dihedral angle restraints: 1973 sinusoidal: 769 harmonic: 1204 Sorted by residual: dihedral pdb=" CA LEU R 461 " pdb=" C LEU R 461 " pdb=" N LYS R 462 " pdb=" CA LYS R 462 " ideal model delta harmonic sigma weight residual 180.00 148.97 31.03 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA GLN B 80 " pdb=" C GLN B 80 " pdb=" N SER B 81 " pdb=" CA SER B 81 " ideal model delta harmonic sigma weight residual -180.00 -152.63 -27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CB CYS R 336 " pdb=" SG CYS R 336 " pdb=" SG CYS R 361 " pdb=" CB CYS R 361 " ideal model delta sinusoidal sigma weight residual -86.00 -131.11 45.11 1 1.00e+01 1.00e-02 2.82e+01 ... (remaining 1970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 320 0.059 - 0.118: 145 0.118 - 0.177: 39 0.177 - 0.235: 6 0.235 - 0.294: 2 Chirality restraints: 512 Sorted by residual: chirality pdb=" CB ILE R 468 " pdb=" CA ILE R 468 " pdb=" CG1 ILE R 468 " pdb=" CG2 ILE R 468 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CG LEU B 96 " pdb=" CB LEU B 96 " pdb=" CD1 LEU B 96 " pdb=" CD2 LEU B 96 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CG LEU B 48 " pdb=" CB LEU B 48 " pdb=" CD1 LEU B 48 " pdb=" CD2 LEU B 48 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 509 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 365 " 0.013 2.00e-02 2.50e+03 2.82e-02 1.59e+01 pdb=" CG TYR R 365 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR R 365 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR R 365 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR R 365 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR R 365 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR R 365 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR R 365 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 369 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.31e+00 pdb=" C TYR R 369 " 0.053 2.00e-02 2.50e+03 pdb=" O TYR R 369 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN R 370 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 88 " 0.017 2.00e-02 2.50e+03 2.05e-02 8.38e+00 pdb=" CG TYR B 88 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR B 88 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 88 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 88 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B 88 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B 88 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 88 " -0.000 2.00e-02 2.50e+03 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 824 2.78 - 3.31: 3092 3.31 - 3.84: 5780 3.84 - 4.37: 6424 4.37 - 4.90: 10952 Nonbonded interactions: 27072 Sorted by model distance: nonbonded pdb=" OG SER R 438 " pdb=" O LYS R 440 " model vdw 2.255 2.440 nonbonded pdb=" OG1 THR B 13 " pdb=" OE1 GLN B 16 " model vdw 2.260 2.440 nonbonded pdb=" O PRO B 7 " pdb=" OG1 THR B 105 " model vdw 2.284 2.440 nonbonded pdb=" OD2 ASP R 398 " pdb=" OH TYR R 423 " model vdw 2.304 2.440 nonbonded pdb=" O TYR R 396 " pdb=" OG SER R 514 " model vdw 2.307 2.440 ... (remaining 27067 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.610 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: 9.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.810 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 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 : 0.009 0.105 3373 Z= 0.578 Angle : 1.316 11.297 4593 Z= 0.709 Chirality : 0.069 0.294 512 Planarity : 0.009 0.067 588 Dihedral : 14.139 72.801 1190 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.73 % Allowed : 11.46 % Favored : 87.80 % Rotamer: Outliers : 0.55 % Allowed : 1.38 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.57 (0.39), residues: 410 helix: -4.65 (0.52), residues: 21 sheet: -0.77 (0.43), residues: 142 loop : -2.08 (0.37), residues: 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 0.396 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 168 average time/residue: 0.1916 time to fit residues: 37.3826 Evaluate side-chains 101 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 334 ASN R 409 GLN ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 39 HIS ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3373 Z= 0.285 Angle : 0.807 9.232 4593 Z= 0.417 Chirality : 0.048 0.211 512 Planarity : 0.008 0.123 588 Dihedral : 7.312 26.854 456 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.49 % Allowed : 8.78 % Favored : 90.73 % Rotamer: Outliers : 0.28 % Allowed : 7.73 % Favored : 91.99 % 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: -2.64 (0.39), residues: 410 helix: -4.61 (0.76), residues: 14 sheet: -1.00 (0.43), residues: 124 loop : -2.06 (0.37), residues: 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 120 average time/residue: 0.1627 time to fit residues: 23.4479 Evaluate side-chains 96 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.385 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0364 time to fit residues: 0.5818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 3373 Z= 0.389 Angle : 0.824 6.624 4593 Z= 0.435 Chirality : 0.048 0.155 512 Planarity : 0.007 0.107 588 Dihedral : 7.072 25.131 456 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 25.79 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.22 % Favored : 88.29 % Rotamer: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % 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: -2.38 (0.41), residues: 410 helix: -4.58 (0.60), residues: 14 sheet: -1.20 (0.43), residues: 140 loop : -1.66 (0.40), residues: 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1696 time to fit residues: 22.0140 Evaluate side-chains 86 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 19 optimal weight: 0.0060 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 0.0770 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 417 ASN R 474 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3373 Z= 0.203 Angle : 0.735 7.146 4593 Z= 0.379 Chirality : 0.046 0.191 512 Planarity : 0.007 0.108 588 Dihedral : 6.428 26.742 456 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.02 % Favored : 90.49 % Rotamer: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % 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: -2.30 (0.41), residues: 410 helix: -4.54 (0.67), residues: 14 sheet: -1.07 (0.44), residues: 139 loop : -1.65 (0.39), residues: 257 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.402 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: 124 average time/residue: 0.1464 time to fit residues: 22.1646 Evaluate side-chains 90 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.0030 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 ASN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3373 Z= 0.227 Angle : 0.724 7.478 4593 Z= 0.374 Chirality : 0.046 0.182 512 Planarity : 0.007 0.091 588 Dihedral : 6.428 27.465 456 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.00 % Favored : 89.51 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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: -2.25 (0.41), residues: 410 helix: -3.99 (0.96), residues: 14 sheet: -0.97 (0.45), residues: 139 loop : -1.69 (0.39), residues: 257 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1547 time to fit residues: 22.5503 Evaluate side-chains 88 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.1980 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3373 Z= 0.226 Angle : 0.732 8.408 4593 Z= 0.372 Chirality : 0.046 0.191 512 Planarity : 0.007 0.115 588 Dihedral : 6.363 26.688 456 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.00 % Favored : 89.76 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: -2.22 (0.41), residues: 410 helix: -3.70 (0.72), residues: 20 sheet: -0.98 (0.45), residues: 139 loop : -1.60 (0.39), residues: 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.379 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: 120 average time/residue: 0.1444 time to fit residues: 21.0976 Evaluate side-chains 92 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.5978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 3373 Z= 0.225 Angle : 0.735 11.343 4593 Z= 0.372 Chirality : 0.046 0.209 512 Planarity : 0.006 0.098 588 Dihedral : 6.430 27.900 456 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.24 % Favored : 89.27 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: -2.18 (0.41), residues: 410 helix: -3.53 (0.82), residues: 20 sheet: -0.90 (0.45), residues: 140 loop : -1.62 (0.40), residues: 250 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1674 time to fit residues: 22.9221 Evaluate side-chains 91 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.0010 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** B 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 3373 Z= 0.213 Angle : 0.723 9.773 4593 Z= 0.367 Chirality : 0.046 0.179 512 Planarity : 0.006 0.089 588 Dihedral : 6.283 28.419 456 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.00 % Favored : 89.51 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: -2.01 (0.41), residues: 410 helix: -3.45 (0.85), residues: 20 sheet: -0.68 (0.46), residues: 135 loop : -1.57 (0.39), residues: 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1436 time to fit residues: 20.7621 Evaluate side-chains 93 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.0030 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.6374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 3373 Z= 0.219 Angle : 0.711 8.324 4593 Z= 0.366 Chirality : 0.046 0.178 512 Planarity : 0.006 0.084 588 Dihedral : 6.322 27.056 456 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.24 % Favored : 89.27 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -2.05 (0.41), residues: 410 helix: -3.43 (0.92), residues: 20 sheet: -0.63 (0.46), residues: 135 loop : -1.65 (0.38), residues: 255 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1621 time to fit residues: 22.2884 Evaluate side-chains 93 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.399 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.6658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3373 Z= 0.230 Angle : 0.732 7.209 4593 Z= 0.372 Chirality : 0.046 0.176 512 Planarity : 0.006 0.082 588 Dihedral : 6.248 26.888 456 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.00 % Favored : 89.76 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.41), residues: 410 helix: -3.60 (0.87), residues: 20 sheet: -0.46 (0.48), residues: 131 loop : -1.57 (0.38), residues: 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1581 time to fit residues: 21.3254 Evaluate side-chains 91 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.0170 chunk 39 optimal weight: 0.9980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.127777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.109932 restraints weight = 8803.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.112978 restraints weight = 5436.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.115160 restraints weight = 3788.394| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.6806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 3373 Z= 0.231 Angle : 0.711 7.154 4593 Z= 0.362 Chirality : 0.046 0.175 512 Planarity : 0.006 0.081 588 Dihedral : 6.244 27.295 456 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.24 % Favored : 89.27 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.41), residues: 410 helix: -3.57 (0.88), residues: 20 sheet: -0.46 (0.47), residues: 135 loop : -1.59 (0.38), residues: 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1404.07 seconds wall clock time: 25 minutes 54.15 seconds (1554.15 seconds total)