Starting phenix.real_space_refine on Sun Mar 10 16:21:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrj_32728/03_2024/7wrj_32728.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrj_32728/03_2024/7wrj_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_32728/03_2024/7wrj_32728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrj_32728/03_2024/7wrj_32728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrj_32728/03_2024/7wrj_32728.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrj_32728/03_2024/7wrj_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-dev-5265/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: 2.47, per 1000 atoms: 0.75 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 623.6 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: 0.34 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: 0.77 Time building geometry restraints manager: 1.51 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.500 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.900 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.330 ------------------------------------------------------------------------------- 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 : 0.391 Fit side-chains revert: symmetry clash REVERT: R 353 TRP cc_start: 0.8506 (p-90) cc_final: 0.7034 (p-90) REVERT: R 387 LEU cc_start: 0.8124 (mp) cc_final: 0.7594 (mp) REVERT: R 396 TYR cc_start: 0.6913 (m-80) cc_final: 0.6704 (m-80) REVERT: R 410 ILE cc_start: 0.8475 (mm) cc_final: 0.8256 (mm) REVERT: R 453 TYR cc_start: 0.7520 (p90) cc_final: 0.7297 (p90) REVERT: R 496 SER cc_start: 0.8448 (t) cc_final: 0.8174 (p) REVERT: A 4 LEU cc_start: 0.8974 (mm) cc_final: 0.8682 (mm) REVERT: A 7 SER cc_start: 0.9348 (p) cc_final: 0.8987 (m) REVERT: A 69 LEU cc_start: 0.8035 (mm) cc_final: 0.7822 (mm) REVERT: A 115 MET cc_start: 0.8302 (tpt) cc_final: 0.7835 (tpp) REVERT: A 121 MET cc_start: 0.6637 (ptt) cc_final: 0.6414 (ppp) REVERT: B 36 TRP cc_start: 0.8302 (m100) cc_final: 0.8068 (m100) REVERT: B 37 TYR cc_start: 0.7704 (m-80) cc_final: 0.7322 (m-80) REVERT: B 90 GLU cc_start: 0.8174 (pt0) cc_final: 0.6755 (pt0) REVERT: B 91 THR cc_start: 0.8922 (m) cc_final: 0.8603 (p) REVERT: B 101 PHE cc_start: 0.8501 (m-80) cc_final: 0.8251 (m-10) REVERT: B 109 VAL cc_start: 0.3809 (p) cc_final: 0.3388 (p) outliers start: 2 outliers final: 0 residues processed: 168 average time/residue: 0.1926 time to fit residues: 37.6944 Evaluate side-chains 102 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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: 0.7980 chunk 30 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 3373 Z= 0.291 Angle : 0.802 10.213 4593 Z= 0.414 Chirality : 0.048 0.197 512 Planarity : 0.008 0.123 588 Dihedral : 7.376 27.364 498 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 23.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.51 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % 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: -2.62 (0.39), residues: 410 helix: -4.48 (0.97), residues: 12 sheet: -0.92 (0.43), residues: 118 loop : -2.11 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 49 HIS 0.006 0.003 HIS A 99 PHE 0.017 0.002 PHE R 377 TYR 0.018 0.002 TYR R 421 ARG 0.004 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 122 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.393 Fit side-chains REVERT: R 353 TRP cc_start: 0.8337 (p-90) cc_final: 0.7647 (p90) REVERT: R 365 TYR cc_start: 0.7661 (m-80) cc_final: 0.7411 (m-80) REVERT: R 428 ASP cc_start: 0.7888 (t0) cc_final: 0.7427 (t0) REVERT: R 496 SER cc_start: 0.8465 (t) cc_final: 0.7881 (p) REVERT: A 4 LEU cc_start: 0.9143 (mm) cc_final: 0.8880 (mm) REVERT: A 7 SER cc_start: 0.9143 (p) cc_final: 0.8870 (m) REVERT: A 61 TYR cc_start: 0.6190 (m-80) cc_final: 0.5878 (m-80) REVERT: A 62 ASN cc_start: 0.9029 (t0) cc_final: 0.8611 (t0) REVERT: A 108 ILE cc_start: 0.8686 (mp) cc_final: 0.8367 (mp) REVERT: A 111 ASP cc_start: 0.9177 (t0) cc_final: 0.8732 (t0) REVERT: A 115 MET cc_start: 0.8421 (tpt) cc_final: 0.8178 (tpp) REVERT: A 121 MET cc_start: 0.7050 (ptt) cc_final: 0.6732 (ppp) REVERT: B 36 TRP cc_start: 0.8263 (m100) cc_final: 0.7988 (m100) REVERT: B 90 GLU cc_start: 0.7895 (pt0) cc_final: 0.7157 (pt0) REVERT: B 99 VAL cc_start: 0.9113 (t) cc_final: 0.8776 (t) REVERT: B 106 ARG cc_start: 0.8801 (mtm110) cc_final: 0.8585 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1600 time to fit residues: 23.5514 Evaluate side-chains 92 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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: 0.4980 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.0670 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 0.0370 chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 0.1980 overall best weight: 0.2796 ------------------------------------------------------------------------------- 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 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3373 Z= 0.184 Angle : 0.708 7.029 4593 Z= 0.366 Chirality : 0.046 0.179 512 Planarity : 0.007 0.101 588 Dihedral : 6.515 27.366 498 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.27 % Favored : 90.24 % Rotamer: Outliers : 0.55 % Allowed : 4.42 % Favored : 95.03 % 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: -2.45 (0.40), residues: 410 helix: -4.65 (0.78), residues: 12 sheet: -1.10 (0.43), residues: 133 loop : -1.84 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 49 HIS 0.008 0.002 HIS B 51 PHE 0.017 0.001 PHE R 377 TYR 0.019 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 127 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 428 ASP cc_start: 0.7966 (t0) cc_final: 0.7339 (t0) REVERT: R 474 GLN cc_start: 0.6047 (OUTLIER) cc_final: 0.5709 (tm-30) REVERT: R 496 SER cc_start: 0.8427 (t) cc_final: 0.8150 (p) REVERT: R 500 THR cc_start: 0.8778 (p) cc_final: 0.7937 (t) REVERT: A 4 LEU cc_start: 0.9147 (mm) cc_final: 0.8923 (mm) REVERT: A 7 SER cc_start: 0.9096 (p) cc_final: 0.8778 (m) REVERT: A 61 TYR cc_start: 0.6456 (m-80) cc_final: 0.6107 (m-80) REVERT: A 62 ASN cc_start: 0.9117 (t0) cc_final: 0.8840 (t0) REVERT: A 108 ILE cc_start: 0.8798 (mp) cc_final: 0.8490 (mp) REVERT: A 111 ASP cc_start: 0.9095 (t0) cc_final: 0.8631 (t0) REVERT: A 115 MET cc_start: 0.8396 (tpt) cc_final: 0.8148 (tpp) REVERT: A 121 MET cc_start: 0.7189 (ptt) cc_final: 0.6703 (ppp) REVERT: B 36 TRP cc_start: 0.8193 (m100) cc_final: 0.7987 (m100) REVERT: B 37 TYR cc_start: 0.7575 (m-80) cc_final: 0.7025 (m-80) REVERT: B 39 HIS cc_start: 0.7354 (t70) cc_final: 0.7032 (t70) REVERT: B 90 GLU cc_start: 0.8034 (pt0) cc_final: 0.7646 (pt0) REVERT: B 106 ARG cc_start: 0.8800 (mtm110) cc_final: 0.8589 (mtm-85) outliers start: 2 outliers final: 0 residues processed: 126 average time/residue: 0.1309 time to fit residues: 20.4081 Evaluate side-chains 98 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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: 2.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 334 ASN A 86 ASN 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: 0.7303 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3373 Z= 0.242 Angle : 0.732 8.752 4593 Z= 0.372 Chirality : 0.046 0.195 512 Planarity : 0.007 0.107 588 Dihedral : 6.579 30.841 498 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.00 % Favored : 89.51 % Rotamer: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % 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: -2.08 (0.42), residues: 410 helix: -4.76 (0.68), residues: 14 sheet: -0.88 (0.45), residues: 136 loop : -1.49 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 38 HIS 0.005 0.002 HIS A 99 PHE 0.018 0.002 PHE R 377 TYR 0.016 0.002 TYR R 489 ARG 0.004 0.001 ARG R 498 *********************** 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 119 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: R 402 ILE cc_start: 0.8867 (tt) cc_final: 0.8591 (tt) REVERT: R 428 ASP cc_start: 0.8111 (t0) cc_final: 0.7457 (t0) REVERT: A 7 SER cc_start: 0.9191 (p) cc_final: 0.8893 (m) REVERT: A 61 TYR cc_start: 0.6727 (m-80) cc_final: 0.6305 (m-80) REVERT: A 62 ASN cc_start: 0.9254 (t0) cc_final: 0.8556 (t0) REVERT: A 108 ILE cc_start: 0.8795 (mp) cc_final: 0.8498 (mp) REVERT: A 111 ASP cc_start: 0.9125 (t0) cc_final: 0.8721 (t0) REVERT: A 121 MET cc_start: 0.7505 (ptt) cc_final: 0.6723 (ppp) REVERT: B 37 TYR cc_start: 0.7378 (m-80) cc_final: 0.6886 (m-10) REVERT: B 49 ILE cc_start: 0.8445 (tp) cc_final: 0.8181 (tp) REVERT: B 90 GLU cc_start: 0.8179 (pt0) cc_final: 0.7908 (pt0) REVERT: B 99 VAL cc_start: 0.9192 (t) cc_final: 0.8816 (t) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1435 time to fit residues: 20.8301 Evaluate side-chains 92 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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: 2.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.0570 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 417 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3373 Z= 0.216 Angle : 0.709 6.688 4593 Z= 0.362 Chirality : 0.046 0.175 512 Planarity : 0.006 0.088 588 Dihedral : 6.455 31.565 498 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.76 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % 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: -2.13 (0.42), residues: 410 helix: -4.70 (0.70), residues: 14 sheet: -0.96 (0.44), residues: 141 loop : -1.50 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 49 HIS 0.005 0.002 HIS A 99 PHE 0.017 0.002 PHE R 377 TYR 0.020 0.002 TYR B 50 ARG 0.004 0.001 ARG R 457 *********************** 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 117 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 428 ASP cc_start: 0.8157 (t0) cc_final: 0.7661 (t70) REVERT: A 7 SER cc_start: 0.9086 (p) cc_final: 0.8799 (m) REVERT: A 61 TYR cc_start: 0.6727 (m-80) cc_final: 0.6316 (m-80) REVERT: A 62 ASN cc_start: 0.9054 (t0) cc_final: 0.8642 (t0) REVERT: A 108 ILE cc_start: 0.8686 (mp) cc_final: 0.8435 (mp) REVERT: A 111 ASP cc_start: 0.9122 (t0) cc_final: 0.8724 (t0) REVERT: A 121 MET cc_start: 0.7446 (ptt) cc_final: 0.6696 (ppp) REVERT: B 36 TRP cc_start: 0.8382 (m100) cc_final: 0.8052 (m100) REVERT: B 48 LEU cc_start: 0.8636 (mm) cc_final: 0.8333 (mt) REVERT: B 49 ILE cc_start: 0.8442 (tp) cc_final: 0.8113 (tt) REVERT: B 86 ASP cc_start: 0.6750 (m-30) cc_final: 0.6524 (m-30) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1583 time to fit residues: 22.3511 Evaluate side-chains 89 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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: 2.9990 chunk 38 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7331 moved from start: 0.5258 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= 0.250 Angle : 0.710 8.163 4593 Z= 0.361 Chirality : 0.046 0.187 512 Planarity : 0.007 0.112 588 Dihedral : 6.582 33.732 498 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.24 % Favored : 89.27 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: -2.09 (0.42), residues: 410 helix: -4.74 (0.65), residues: 14 sheet: -0.90 (0.45), residues: 141 loop : -1.50 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 49 HIS 0.005 0.002 HIS A 99 PHE 0.017 0.002 PHE R 377 TYR 0.013 0.002 TYR R 421 ARG 0.004 0.001 ARG R 454 *********************** 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 : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 428 ASP cc_start: 0.8272 (t0) cc_final: 0.7717 (t70) REVERT: R 500 THR cc_start: 0.8765 (p) cc_final: 0.8236 (t) REVERT: A 7 SER cc_start: 0.9122 (p) cc_final: 0.8833 (m) REVERT: A 61 TYR cc_start: 0.6803 (m-80) cc_final: 0.6278 (m-80) REVERT: A 62 ASN cc_start: 0.9139 (t0) cc_final: 0.8571 (t0) REVERT: A 96 PHE cc_start: 0.9137 (m-80) cc_final: 0.8908 (m-10) REVERT: A 108 ILE cc_start: 0.8690 (mp) cc_final: 0.8385 (mp) REVERT: A 111 ASP cc_start: 0.9175 (t0) cc_final: 0.8926 (t0) REVERT: A 121 MET cc_start: 0.7542 (ptt) cc_final: 0.6804 (ppp) REVERT: B 48 LEU cc_start: 0.8665 (mm) cc_final: 0.8354 (mt) REVERT: B 49 ILE cc_start: 0.8240 (tp) cc_final: 0.8014 (tp) REVERT: B 86 ASP cc_start: 0.6693 (m-30) cc_final: 0.6429 (m-30) REVERT: B 90 GLU cc_start: 0.8232 (pt0) cc_final: 0.7376 (pt0) REVERT: B 99 VAL cc_start: 0.9128 (t) cc_final: 0.8656 (t) REVERT: B 109 VAL cc_start: 0.4835 (p) cc_final: 0.4607 (p) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1390 time to fit residues: 19.6675 Evaluate side-chains 89 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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: 3.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.0570 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.0030 overall best weight: 0.3686 ------------------------------------------------------------------------------- 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: 0.7286 moved from start: 0.5449 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= 0.179 Angle : 0.700 6.542 4593 Z= 0.354 Chirality : 0.046 0.187 512 Planarity : 0.006 0.094 588 Dihedral : 6.374 33.987 498 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.49 % Allowed : 8.29 % Favored : 91.22 % 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: -2.03 (0.42), residues: 410 helix: -3.71 (0.85), residues: 20 sheet: -0.81 (0.46), residues: 135 loop : -1.48 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 49 HIS 0.005 0.001 HIS A 99 PHE 0.014 0.001 PHE R 377 TYR 0.010 0.001 TYR R 423 ARG 0.004 0.000 ARG R 498 *********************** 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 120 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 386 LYS cc_start: 0.7860 (pttt) cc_final: 0.7567 (pttp) REVERT: R 428 ASP cc_start: 0.8209 (t0) cc_final: 0.7637 (t70) REVERT: R 500 THR cc_start: 0.8728 (p) cc_final: 0.8196 (t) REVERT: A 7 SER cc_start: 0.9125 (p) cc_final: 0.8752 (m) REVERT: A 108 ILE cc_start: 0.8631 (mp) cc_final: 0.8409 (mp) REVERT: A 111 ASP cc_start: 0.9150 (t0) cc_final: 0.8898 (t0) REVERT: A 121 MET cc_start: 0.7454 (ptt) cc_final: 0.6715 (ppp) REVERT: B 49 ILE cc_start: 0.8201 (tp) cc_final: 0.7997 (tp) REVERT: B 86 ASP cc_start: 0.6738 (m-30) cc_final: 0.6523 (m-30) REVERT: B 90 GLU cc_start: 0.8191 (pt0) cc_final: 0.7451 (pt0) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1413 time to fit residues: 20.9115 Evaluate side-chains 97 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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: 0.2980 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 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 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 417 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3373 Z= 0.219 Angle : 0.681 6.071 4593 Z= 0.350 Chirality : 0.046 0.179 512 Planarity : 0.006 0.086 588 Dihedral : 6.448 36.378 498 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.76 % Favored : 90.00 % 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 : 0.00 % 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: -2.08 (0.42), residues: 410 helix: -3.85 (0.85), residues: 20 sheet: -0.90 (0.46), residues: 136 loop : -1.46 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 49 HIS 0.004 0.002 HIS A 99 PHE 0.021 0.002 PHE A 96 TYR 0.011 0.002 TYR R 495 ARG 0.004 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 121 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 386 LYS cc_start: 0.7948 (pttt) cc_final: 0.7649 (pttp) REVERT: R 409 GLN cc_start: 0.8877 (mm110) cc_final: 0.8278 (mm-40) REVERT: R 428 ASP cc_start: 0.8207 (t0) cc_final: 0.7652 (t70) REVERT: R 500 THR cc_start: 0.8736 (p) cc_final: 0.8161 (t) REVERT: A 7 SER cc_start: 0.9291 (p) cc_final: 0.8930 (m) REVERT: A 11 LEU cc_start: 0.7695 (pt) cc_final: 0.7494 (mp) REVERT: A 61 TYR cc_start: 0.6183 (m-80) cc_final: 0.5904 (m-80) REVERT: A 62 ASN cc_start: 0.8918 (t0) cc_final: 0.8344 (t0) REVERT: A 66 LYS cc_start: 0.8841 (mmpt) cc_final: 0.8630 (mmmt) REVERT: A 108 ILE cc_start: 0.8583 (mp) cc_final: 0.8360 (mp) REVERT: A 121 MET cc_start: 0.7596 (ptt) cc_final: 0.6924 (ppp) REVERT: B 86 ASP cc_start: 0.6657 (m-30) cc_final: 0.6454 (m-30) REVERT: B 90 GLU cc_start: 0.8193 (pt0) cc_final: 0.7419 (pt0) REVERT: B 99 VAL cc_start: 0.9065 (t) cc_final: 0.8607 (t) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1397 time to fit residues: 20.9190 Evaluate side-chains 96 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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: 0.1980 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 409 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: 0.7359 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3373 Z= 0.224 Angle : 0.681 5.964 4593 Z= 0.349 Chirality : 0.046 0.174 512 Planarity : 0.006 0.081 588 Dihedral : 6.401 36.851 498 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.51 % Favored : 90.00 % 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: -2.01 (0.42), residues: 410 helix: -3.90 (0.81), residues: 20 sheet: -0.77 (0.46), residues: 135 loop : -1.46 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 36 HIS 0.005 0.001 HIS A 99 PHE 0.022 0.002 PHE R 377 TYR 0.025 0.002 TYR B 50 ARG 0.005 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 115 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 386 LYS cc_start: 0.7986 (pttt) cc_final: 0.7722 (pttp) REVERT: R 409 GLN cc_start: 0.8925 (mm110) cc_final: 0.8599 (mm-40) REVERT: R 428 ASP cc_start: 0.8276 (t0) cc_final: 0.7714 (t70) REVERT: R 443 SER cc_start: 0.8309 (p) cc_final: 0.7898 (t) REVERT: R 500 THR cc_start: 0.8802 (p) cc_final: 0.8231 (t) REVERT: A 7 SER cc_start: 0.9266 (p) cc_final: 0.8914 (m) REVERT: A 62 ASN cc_start: 0.8921 (t0) cc_final: 0.8475 (t0) REVERT: A 66 LYS cc_start: 0.8832 (mmpt) cc_final: 0.8626 (mmmt) REVERT: A 96 PHE cc_start: 0.9070 (m-10) cc_final: 0.8816 (m-10) REVERT: A 121 MET cc_start: 0.7604 (ptt) cc_final: 0.6962 (ppp) REVERT: B 84 GLU cc_start: 0.7492 (mp0) cc_final: 0.7278 (mp0) REVERT: B 86 ASP cc_start: 0.6601 (m-30) cc_final: 0.6394 (m-30) REVERT: B 90 GLU cc_start: 0.8241 (pt0) cc_final: 0.7644 (pt0) REVERT: B 93 ASP cc_start: 0.7472 (t0) cc_final: 0.7115 (t0) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1374 time to fit residues: 19.5456 Evaluate side-chains 94 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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: 2.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 409 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: 0.7348 moved from start: 0.6143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 3373 Z= 0.246 Angle : 0.719 5.599 4593 Z= 0.368 Chirality : 0.047 0.214 512 Planarity : 0.006 0.079 588 Dihedral : 6.766 37.779 498 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.00 % Favored : 89.51 % 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: -2.08 (0.42), residues: 410 helix: -3.93 (0.80), residues: 20 sheet: -0.82 (0.46), residues: 135 loop : -1.51 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 36 HIS 0.005 0.002 HIS B 51 PHE 0.018 0.002 PHE R 377 TYR 0.012 0.002 TYR A 61 ARG 0.005 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 : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 386 LYS cc_start: 0.7961 (pttt) cc_final: 0.7755 (pttp) REVERT: R 387 LEU cc_start: 0.8148 (mp) cc_final: 0.7928 (mp) REVERT: R 428 ASP cc_start: 0.8324 (t0) cc_final: 0.7776 (t70) REVERT: R 443 SER cc_start: 0.8268 (p) cc_final: 0.7873 (t) REVERT: R 500 THR cc_start: 0.8826 (p) cc_final: 0.8285 (t) REVERT: A 7 SER cc_start: 0.9280 (p) cc_final: 0.8905 (m) REVERT: A 62 ASN cc_start: 0.8970 (t0) cc_final: 0.8565 (t0) REVERT: A 66 LYS cc_start: 0.8808 (mmpt) cc_final: 0.8597 (mmmt) REVERT: A 121 MET cc_start: 0.7589 (ptt) cc_final: 0.6949 (ppp) REVERT: B 90 GLU cc_start: 0.8173 (pt0) cc_final: 0.7689 (pt0) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1433 time to fit residues: 20.5660 Evaluate side-chains 92 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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: 0.6980 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 51 HIS ** 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 = 0.3826 r_free = 0.3826 target = 0.130191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.112441 restraints weight = 8495.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.115593 restraints weight = 5091.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.117799 restraints weight = 3481.402| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.6449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3373 Z= 0.254 Angle : 0.746 10.600 4593 Z= 0.377 Chirality : 0.048 0.219 512 Planarity : 0.006 0.078 588 Dihedral : 6.895 39.195 498 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 21.31 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 : 0.51 % 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: -2.20 (0.42), residues: 410 helix: -4.32 (0.58), residues: 26 sheet: -0.74 (0.46), residues: 141 loop : -1.59 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 36 HIS 0.008 0.002 HIS B 51 PHE 0.018 0.002 PHE R 377 TYR 0.029 0.002 TYR B 50 ARG 0.005 0.001 ARG B 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1432.40 seconds wall clock time: 26 minutes 22.22 seconds (1582.22 seconds total)