Starting phenix.real_space_refine on Thu Dec 7 17:46:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrj_32728/12_2023/7wrj_32728.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrj_32728/12_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_32728/12_2023/7wrj_32728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrj_32728/12_2023/7wrj_32728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrj_32728/12_2023/7wrj_32728.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrj_32728/12_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-1.21rc1-5172/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.35, per 1000 atoms: 0.71 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: 1.35 Conformation dependent library (CDL) restraints added in 600.7 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: 0.44 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: 0.84 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: 1701 14.56 - 29.12: 247 29.12 - 43.68: 52 43.68 - 58.24: 10 58.24 - 72.80: 5 Dihedral angle restraints: 2015 sinusoidal: 811 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 2012 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: 2.150 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: 9.660 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.020 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.740 ------------------------------------------------------------------------------- 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 : 14.006 72.801 1232 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP A 55 HIS 0.011 0.003 HIS R 505 PHE 0.034 0.004 PHE A 96 TYR 0.066 0.005 TYR R 365 ARG 0.013 0.002 ARG R 408 *********************** 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: 0.1906 time to fit residues: 37.1653 Evaluate side-chains 101 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5281 ------------------------------------------------------------------------------- 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 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 3373 Z= 0.292 Angle : 0.807 10.073 4593 Z= 0.415 Chirality : 0.048 0.188 512 Planarity : 0.008 0.125 588 Dihedral : 7.413 27.054 498 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.02 % Favored : 90.73 % Rotamer: Outliers : 0.28 % Allowed : 7.46 % Favored : 92.27 % 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: -2.65 (0.39), residues: 410 helix: -4.53 (0.84), residues: 14 sheet: -1.01 (0.43), residues: 124 loop : -2.07 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 49 HIS 0.006 0.003 HIS A 99 PHE 0.016 0.002 PHE R 377 TYR 0.018 0.002 TYR R 421 ARG 0.005 0.001 ARG R 466 *********************** 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 : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 120 average time/residue: 0.1660 time to fit residues: 24.0021 Evaluate side-chains 95 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.410 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0320 time to fit residues: 0.5915 ------------------------------------------------------------------------------- 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: 5.9990 chunk 24 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 474 GLN B 6 GLN B 38 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: 0.7239 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3373 Z= 0.223 Angle : 0.730 6.568 4593 Z= 0.378 Chirality : 0.046 0.176 512 Planarity : 0.007 0.104 588 Dihedral : 6.726 28.777 498 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.51 % Favored : 90.00 % Rotamer: Outliers : 0.28 % Allowed : 3.87 % Favored : 95.86 % 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: -2.40 (0.41), residues: 410 helix: -4.62 (0.75), residues: 12 sheet: -1.01 (0.44), residues: 133 loop : -1.83 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 49 HIS 0.005 0.002 HIS A 99 PHE 0.016 0.001 PHE R 377 TYR 0.016 0.002 TYR B 50 ARG 0.004 0.001 ARG R 408 *********************** 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 111 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 0.389 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.1529 time to fit residues: 20.5226 Evaluate side-chains 88 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.316 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3911 ------------------------------------------------------------------------------- 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: 0.5980 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 36 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN B 6 GLN B 38 GLN ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3373 Z= 0.214 Angle : 0.718 7.896 4593 Z= 0.366 Chirality : 0.046 0.185 512 Planarity : 0.006 0.109 588 Dihedral : 6.551 30.638 498 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.76 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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: -2.24 (0.41), residues: 410 helix: -4.57 (0.78), residues: 12 sheet: -0.91 (0.44), residues: 137 loop : -1.71 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 36 HIS 0.005 0.002 HIS A 99 PHE 0.017 0.002 PHE R 377 TYR 0.015 0.002 TYR A 61 ARG 0.003 0.001 ARG R 408 *********************** 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 118 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.415 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1522 time to fit residues: 21.8838 Evaluate side-chains 88 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.415 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5010 ------------------------------------------------------------------------------- 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: 0.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.0570 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3373 Z= 0.290 Angle : 0.754 7.020 4593 Z= 0.386 Chirality : 0.047 0.182 512 Planarity : 0.007 0.091 588 Dihedral : 6.866 34.707 498 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.24 % Favored : 89.27 % Rotamer: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % 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: -4.57 (0.67), residues: 14 sheet: -0.92 (0.44), residues: 140 loop : -1.60 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 49 HIS 0.005 0.002 HIS A 99 PHE 0.018 0.002 PHE R 456 TYR 0.023 0.002 TYR B 50 ARG 0.009 0.001 ARG A 40 *********************** 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 115 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1607 time to fit residues: 22.2899 Evaluate side-chains 90 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.424 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5527 ------------------------------------------------------------------------------- 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: 0.1980 chunk 38 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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: 0.7357 moved from start: 0.5676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3373 Z= 0.229 Angle : 0.735 6.724 4593 Z= 0.373 Chirality : 0.047 0.173 512 Planarity : 0.006 0.084 588 Dihedral : 6.599 35.439 498 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.51 % Favored : 90.00 % 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: -2.07 (0.41), residues: 410 helix: -3.41 (0.92), residues: 20 sheet: -0.87 (0.44), residues: 142 loop : -1.52 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 36 HIS 0.005 0.002 HIS A 99 PHE 0.013 0.001 PHE A 24 TYR 0.014 0.002 TYR R 423 ARG 0.008 0.001 ARG R 457 *********************** 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 115 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1463 time to fit residues: 20.8696 Evaluate side-chains 90 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4689 ------------------------------------------------------------------------------- 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: 0.1980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.0170 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.0170 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 0.0570 overall best weight: 0.1374 ------------------------------------------------------------------------------- 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: 0.7283 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3373 Z= 0.179 Angle : 0.701 9.135 4593 Z= 0.350 Chirality : 0.045 0.197 512 Planarity : 0.007 0.117 588 Dihedral : 6.391 35.504 498 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.27 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % 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: -2.04 (0.41), residues: 410 helix: -3.16 (1.01), residues: 18 sheet: -0.76 (0.44), residues: 141 loop : -1.61 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 36 HIS 0.005 0.002 HIS A 99 PHE 0.018 0.001 PHE A 96 TYR 0.013 0.002 TYR A 61 ARG 0.005 0.001 ARG A 40 *********************** 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 124 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1450 time to fit residues: 22.0478 Evaluate side-chains 102 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5318 ------------------------------------------------------------------------------- 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: 0.6980 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.7377 moved from start: 0.6124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3373 Z= 0.256 Angle : 0.720 6.749 4593 Z= 0.367 Chirality : 0.046 0.180 512 Planarity : 0.007 0.102 588 Dihedral : 6.654 38.143 498 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.51 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -2.02 (0.41), residues: 410 helix: -3.73 (0.78), residues: 20 sheet: -0.76 (0.44), residues: 142 loop : -1.51 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B 36 HIS 0.005 0.002 HIS A 99 PHE 0.018 0.002 PHE R 377 TYR 0.015 0.002 TYR R 423 ARG 0.005 0.001 ARG B 106 *********************** 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 119 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1507 time to fit residues: 22.1053 Evaluate side-chains 91 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.400 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5256 ------------------------------------------------------------------------------- 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: 0.5980 chunk 23 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** B 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.6424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3373 Z= 0.205 Angle : 0.692 5.862 4593 Z= 0.350 Chirality : 0.045 0.182 512 Planarity : 0.006 0.093 588 Dihedral : 6.476 38.378 498 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.51 % Favored : 90.00 % 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: -2.12 (0.42), residues: 410 helix: -4.19 (0.57), residues: 26 sheet: -0.76 (0.44), residues: 142 loop : -1.49 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 36 HIS 0.008 0.003 HIS B 51 PHE 0.015 0.002 PHE R 377 TYR 0.012 0.002 TYR R 423 ARG 0.004 0.001 ARG B 106 *********************** 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 119 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1455 time to fit residues: 21.1365 Evaluate side-chains 96 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5260 ------------------------------------------------------------------------------- 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: 0.6980 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.0570 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.3498 ------------------------------------------------------------------------------- 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** B 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 3373 Z= 0.206 Angle : 0.711 5.842 4593 Z= 0.361 Chirality : 0.045 0.178 512 Planarity : 0.006 0.088 588 Dihedral : 6.705 38.601 498 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.75 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 : 0.26 % 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: -2.08 (0.42), residues: 410 helix: -4.06 (0.64), residues: 26 sheet: -0.58 (0.45), residues: 138 loop : -1.58 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP B 36 HIS 0.006 0.002 HIS B 51 PHE 0.015 0.001 PHE R 377 TYR 0.010 0.001 TYR R 423 ARG 0.004 0.001 ARG B 106 ********************** 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 117 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 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: 117 average time/residue: 0.1459 time to fit residues: 20.8204 Evaluate side-chains 95 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6167 ------------------------------------------------------------------------------- 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: 9.9990 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** B 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.131790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.113884 restraints weight = 8525.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.116997 restraints weight = 5167.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.119208 restraints weight = 3559.896| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.6758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 3373 Z= 0.250 Angle : 0.739 11.733 4593 Z= 0.376 Chirality : 0.047 0.198 512 Planarity : 0.006 0.085 588 Dihedral : 6.856 39.685 498 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.76 % Favored : 89.76 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: -2.11 (0.41), residues: 410 helix: -4.10 (0.63), residues: 26 sheet: -0.66 (0.45), residues: 142 loop : -1.57 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 36 HIS 0.005 0.002 HIS A 99 PHE 0.016 0.001 PHE R 377 TYR 0.013 0.001 TYR R 423 ARG 0.004 0.001 ARG B 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1388.56 seconds wall clock time: 25 minutes 34.83 seconds (1534.83 seconds total)