Starting phenix.real_space_refine on Sun Mar 10 16:06:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wck_32423/03_2024/7wck_32423.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wck_32423/03_2024/7wck_32423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wck_32423/03_2024/7wck_32423.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wck_32423/03_2024/7wck_32423.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wck_32423/03_2024/7wck_32423.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wck_32423/03_2024/7wck_32423.pdb" } resolution = 3.49 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= 0.041 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 18 5.16 5 C 2049 2.51 5 N 560 2.21 5 O 618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "R ARG 357": "NH1" <-> "NH2" Residue "R GLU 406": "OE1" <-> "OE2" Residue "R GLU 484": "OE1" <-> "OE2" 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: 3245 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 927 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "B" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "R" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1496 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 9, 'TRANS': 178} Chain breaks: 1 Time building chain proxies: 2.22, per 1000 atoms: 0.68 Number of scatterers: 3245 At special positions: 0 Unit cell: (72.36, 85.32, 87.48, 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 18 16.00 O 618 8.00 N 560 7.00 C 2049 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 106 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.04 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=2.06 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 600.0 milliseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 11 sheets defined 10.1% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 4.090A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 33 removed outlier: 3.839A pdb=" N SER B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 33 " --> pdb=" O ARG B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 33' Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.635A pdb=" N PHE B 84 " --> pdb=" O PRO B 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 386 through 390 removed outlier: 3.747A pdb=" N ASP R 389 " --> pdb=" O LYS R 386 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU R 390 " --> pdb=" O LEU R 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 386 through 390' Processing helix chain 'R' and resid 405 through 408 removed outlier: 3.956A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 405 through 408' Processing helix chain 'R' and resid 417 through 422 Processing helix chain 'R' and resid 438 through 443 removed outlier: 3.656A pdb=" N SER R 443 " --> pdb=" O ASN R 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.595A pdb=" N GLU A 10 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 52 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN A 57 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 removed outlier: 5.772A pdb=" N LEU B 11 " --> pdb=" O GLU B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 21 removed outlier: 3.595A pdb=" N ALA B 19 " --> pdb=" O ILE B 76 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.494A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 86 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 357 through 358 removed outlier: 3.633A pdb=" N GLY R 431 " --> pdb=" O TYR R 380 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR R 380 " --> pdb=" O GLY R 431 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL R 433 " --> pdb=" O LYS R 378 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS R 378 " --> pdb=" O VAL R 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.746A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'R' and resid 473 through 474 81 hydrogen bonds defined for protein. 198 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: 0.80 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 525 1.30 - 1.45: 1003 1.45 - 1.59: 1774 1.59 - 1.73: 0 1.73 - 1.87: 22 Bond restraints: 3324 Sorted by residual: bond pdb=" CA HIS B 92 " pdb=" C HIS B 92 " ideal model delta sigma weight residual 1.526 1.376 0.150 1.11e-02 8.12e+03 1.84e+02 bond pdb=" N HIS B 92 " pdb=" CA HIS B 92 " ideal model delta sigma weight residual 1.462 1.351 0.111 1.38e-02 5.25e+03 6.47e+01 bond pdb=" C TRP B 98 " pdb=" O TRP B 98 " ideal model delta sigma weight residual 1.235 1.167 0.068 1.26e-02 6.30e+03 2.90e+01 bond pdb=" C HIS B 92 " pdb=" O HIS B 92 " ideal model delta sigma weight residual 1.231 1.164 0.067 1.41e-02 5.03e+03 2.27e+01 bond pdb=" C GLN B 91 " pdb=" N HIS B 92 " ideal model delta sigma weight residual 1.333 1.281 0.052 1.33e-02 5.65e+03 1.55e+01 ... (remaining 3319 not shown) Histogram of bond angle deviations from ideal: 78.84 - 89.98: 1 89.98 - 101.12: 2 101.12 - 112.26: 1583 112.26 - 123.41: 2746 123.41 - 134.55: 181 Bond angle restraints: 4513 Sorted by residual: angle pdb=" C PRO B 96 " pdb=" N PRO B 97 " pdb=" CD PRO B 97 " ideal model delta sigma weight residual 125.00 78.84 46.16 4.10e+00 5.95e-02 1.27e+02 angle pdb=" C GLN B 91 " pdb=" N HIS B 92 " pdb=" CA HIS B 92 " ideal model delta sigma weight residual 122.41 111.77 10.64 1.41e+00 5.03e-01 5.70e+01 angle pdb=" CA CYS R 432 " pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 114.40 125.81 -11.41 2.30e+00 1.89e-01 2.46e+01 angle pdb=" CB ARG B 78 " pdb=" CG ARG B 78 " pdb=" CD ARG B 78 " ideal model delta sigma weight residual 111.30 121.52 -10.22 2.30e+00 1.89e-01 1.98e+01 angle pdb=" CA GLN B 91 " pdb=" CB GLN B 91 " pdb=" CG GLN B 91 " ideal model delta sigma weight residual 114.10 122.96 -8.86 2.00e+00 2.50e-01 1.96e+01 ... (remaining 4508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 1761 17.96 - 35.92: 174 35.92 - 53.88: 25 53.88 - 71.83: 8 71.83 - 89.79: 1 Dihedral angle restraints: 1969 sinusoidal: 769 harmonic: 1200 Sorted by residual: dihedral pdb=" CA SER B 7 " pdb=" C SER B 7 " pdb=" N PRO B 8 " pdb=" CA PRO B 8 " ideal model delta harmonic sigma weight residual -180.00 -121.83 -58.17 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CB CYS R 480 " pdb=" SG CYS R 480 " pdb=" SG CYS R 488 " pdb=" CB CYS R 488 " ideal model delta sinusoidal sigma weight residual -86.00 -147.09 61.09 1 1.00e+01 1.00e-02 4.96e+01 dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual 93.00 47.85 45.15 1 1.00e+01 1.00e-02 2.83e+01 ... (remaining 1966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 415 0.089 - 0.178: 62 0.178 - 0.267: 8 0.267 - 0.356: 0 0.356 - 0.445: 2 Chirality restraints: 487 Sorted by residual: chirality pdb=" CA HIS B 92 " pdb=" N HIS B 92 " pdb=" C HIS B 92 " pdb=" CB HIS B 92 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CA ASN A 103 " pdb=" N ASN A 103 " pdb=" C ASN A 103 " pdb=" CB ASN A 103 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA PRO B 97 " pdb=" N PRO B 97 " pdb=" C PRO B 97 " pdb=" CB PRO B 97 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 484 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 96 " -0.156 5.00e-02 4.00e+02 2.34e-01 8.79e+01 pdb=" N PRO B 97 " 0.402 5.00e-02 4.00e+02 pdb=" CA PRO B 97 " -0.166 5.00e-02 4.00e+02 pdb=" CD PRO B 97 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 7 " -0.064 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PRO B 8 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 8 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 8 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 13 " -0.051 5.00e-02 4.00e+02 7.74e-02 9.59e+00 pdb=" N PRO A 14 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 14 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 14 " -0.043 5.00e-02 4.00e+02 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 65 2.63 - 3.19: 2733 3.19 - 3.76: 5173 3.76 - 4.33: 7045 4.33 - 4.90: 11712 Nonbonded interactions: 26728 Sorted by model distance: nonbonded pdb=" O HIS B 92 " pdb=" ND1 HIS B 92 " model vdw 2.057 2.520 nonbonded pdb=" OG SER B 95 " pdb=" CD PRO B 96 " model vdw 2.077 3.440 nonbonded pdb=" O PRO B 97 " pdb=" N THR B 99 " model vdw 2.111 2.520 nonbonded pdb=" O PRO B 97 " pdb=" OG1 THR B 99 " model vdw 2.133 2.440 nonbonded pdb=" CB PRO B 96 " pdb=" CD PRO B 97 " model vdw 2.167 3.840 ... (remaining 26723 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 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: 12.980 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.300 Find NCS groups from input model: 0.080 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 : 0.008 0.150 3324 Z= 0.529 Angle : 1.350 46.164 4513 Z= 0.651 Chirality : 0.067 0.445 487 Planarity : 0.013 0.234 585 Dihedral : 13.906 89.789 1182 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 1.72 % Allowed : 7.60 % Favored : 90.69 % Rotamer: Outliers : 0.28 % Allowed : 0.84 % Favored : 98.88 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.39), residues: 408 helix: -4.73 (0.33), residues: 26 sheet: -1.54 (0.47), residues: 136 loop : -2.09 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 98 HIS 0.012 0.005 HIS B 92 PHE 0.014 0.002 PHE R 429 TYR 0.023 0.002 TYR R 369 ARG 0.021 0.002 ARG R 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7232 (ttp-170) cc_final: 0.6927 (ttt-90) REVERT: R 389 ASP cc_start: 0.8117 (p0) cc_final: 0.7656 (p0) outliers start: 1 outliers final: 0 residues processed: 73 average time/residue: 0.2334 time to fit residues: 19.6796 Evaluate side-chains 53 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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: 7.9990 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3324 Z= 0.254 Angle : 0.698 8.711 4513 Z= 0.368 Chirality : 0.049 0.326 487 Planarity : 0.009 0.148 585 Dihedral : 5.956 43.324 458 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.35 % Favored : 91.91 % Rotamer: Outliers : 2.25 % Allowed : 11.24 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -2.86 (0.41), residues: 408 helix: -4.07 (0.53), residues: 32 sheet: -1.37 (0.44), residues: 147 loop : -1.92 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 98 HIS 0.007 0.002 HIS B 92 PHE 0.008 0.001 PHE R 392 TYR 0.024 0.001 TYR B 50 ARG 0.003 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 389 ASP cc_start: 0.8144 (p0) cc_final: 0.7661 (p0) REVERT: R 428 ASP cc_start: 0.8100 (p0) cc_final: 0.7778 (p0) outliers start: 8 outliers final: 2 residues processed: 68 average time/residue: 0.2617 time to fit residues: 21.1043 Evaluate side-chains 54 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain R residue 427 ASP 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: 5.9990 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 39 optimal weight: 0.0970 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 0.0870 chunk 18 optimal weight: 9.9990 overall best weight: 1.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 3324 Z= 0.317 Angle : 0.708 7.296 4513 Z= 0.373 Chirality : 0.050 0.292 487 Planarity : 0.008 0.141 585 Dihedral : 5.784 41.038 458 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.74 % Allowed : 9.31 % Favored : 89.95 % Rotamer: Outliers : 3.09 % Allowed : 13.48 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -2.70 (0.41), residues: 408 helix: -3.98 (0.61), residues: 26 sheet: -1.45 (0.43), residues: 148 loop : -1.75 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP R 436 HIS 0.010 0.003 HIS B 92 PHE 0.012 0.002 PHE R 392 TYR 0.012 0.001 TYR R 453 ARG 0.004 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: R 389 ASP cc_start: 0.8187 (p0) cc_final: 0.7836 (p0) REVERT: R 428 ASP cc_start: 0.8203 (p0) cc_final: 0.7880 (p0) outliers start: 11 outliers final: 6 residues processed: 63 average time/residue: 0.2288 time to fit residues: 16.6756 Evaluate side-chains 56 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 430 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 0.0870 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3324 Z= 0.194 Angle : 0.673 8.360 4513 Z= 0.340 Chirality : 0.048 0.277 487 Planarity : 0.007 0.139 585 Dihedral : 5.231 34.120 458 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.74 % Allowed : 6.62 % Favored : 92.65 % Rotamer: Outliers : 2.25 % Allowed : 17.70 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.41), residues: 408 helix: -3.82 (0.60), residues: 32 sheet: -1.34 (0.43), residues: 147 loop : -1.69 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 436 HIS 0.006 0.002 HIS B 92 PHE 0.009 0.001 PHE R 392 TYR 0.008 0.001 TYR A 80 ARG 0.006 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.405 Fit side-chains REVERT: B 105 LYS cc_start: 0.8506 (tppt) cc_final: 0.8304 (tppt) REVERT: R 389 ASP cc_start: 0.8188 (p0) cc_final: 0.7858 (p0) REVERT: R 428 ASP cc_start: 0.8231 (p0) cc_final: 0.7897 (p0) outliers start: 8 outliers final: 7 residues processed: 67 average time/residue: 0.2091 time to fit residues: 16.4285 Evaluate side-chains 62 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 432 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.0010 chunk 7 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3324 Z= 0.211 Angle : 0.660 9.212 4513 Z= 0.334 Chirality : 0.048 0.285 487 Planarity : 0.007 0.138 585 Dihedral : 5.035 28.755 458 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.35 % Favored : 91.91 % Rotamer: Outliers : 3.65 % Allowed : 17.42 % Favored : 78.93 % 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: -2.57 (0.40), residues: 408 helix: -3.79 (0.71), residues: 26 sheet: -1.30 (0.43), residues: 149 loop : -1.72 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 436 HIS 0.006 0.002 HIS B 92 PHE 0.009 0.001 PHE R 392 TYR 0.022 0.001 TYR B 50 ARG 0.006 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.383 Fit side-chains REVERT: R 389 ASP cc_start: 0.8122 (p0) cc_final: 0.7785 (p0) REVERT: R 408 ARG cc_start: 0.8069 (ptm-80) cc_final: 0.7588 (tmm-80) REVERT: R 428 ASP cc_start: 0.8251 (p0) cc_final: 0.7897 (p0) outliers start: 13 outliers final: 10 residues processed: 64 average time/residue: 0.2119 time to fit residues: 15.8197 Evaluate side-chains 60 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3324 Z= 0.204 Angle : 0.699 14.408 4513 Z= 0.341 Chirality : 0.048 0.289 487 Planarity : 0.008 0.159 585 Dihedral : 4.858 22.202 458 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.11 % Favored : 92.16 % Rotamer: Outliers : 3.37 % Allowed : 17.13 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.41), residues: 408 helix: -3.80 (0.70), residues: 26 sheet: -1.20 (0.44), residues: 147 loop : -1.70 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 436 HIS 0.006 0.002 HIS B 92 PHE 0.008 0.001 PHE R 392 TYR 0.010 0.001 TYR A 80 ARG 0.008 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: B 18 ARG cc_start: 0.7992 (mmm-85) cc_final: 0.7654 (mmm-85) REVERT: R 389 ASP cc_start: 0.8079 (p0) cc_final: 0.7671 (p0) REVERT: R 428 ASP cc_start: 0.8296 (p0) cc_final: 0.7934 (p0) outliers start: 12 outliers final: 7 residues processed: 66 average time/residue: 0.2367 time to fit residues: 18.0694 Evaluate side-chains 62 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 432 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3324 Z= 0.235 Angle : 0.671 9.061 4513 Z= 0.341 Chirality : 0.046 0.137 487 Planarity : 0.005 0.045 585 Dihedral : 4.852 27.451 458 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.35 % Favored : 92.16 % Rotamer: Outliers : 3.65 % Allowed : 17.70 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.40), residues: 408 helix: -3.74 (0.72), residues: 26 sheet: -1.19 (0.44), residues: 147 loop : -1.70 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 98 HIS 0.007 0.002 HIS B 92 PHE 0.030 0.001 PHE A 64 TYR 0.012 0.001 TYR B 50 ARG 0.008 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: B 90 GLN cc_start: 0.7774 (tp-100) cc_final: 0.7538 (tp40) REVERT: R 389 ASP cc_start: 0.8057 (p0) cc_final: 0.7607 (p0) REVERT: R 408 ARG cc_start: 0.8102 (ptm-80) cc_final: 0.7629 (tmm-80) REVERT: R 428 ASP cc_start: 0.8324 (p0) cc_final: 0.7952 (p0) outliers start: 13 outliers final: 9 residues processed: 67 average time/residue: 0.2276 time to fit residues: 17.6292 Evaluate side-chains 61 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 432 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3324 Z= 0.307 Angle : 0.722 10.576 4513 Z= 0.368 Chirality : 0.047 0.143 487 Planarity : 0.005 0.044 585 Dihedral : 4.963 22.175 458 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.49 % Allowed : 8.33 % Favored : 91.18 % Rotamer: Outliers : 3.09 % Allowed : 18.82 % Favored : 78.09 % 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: -2.59 (0.40), residues: 408 helix: -3.66 (0.72), residues: 26 sheet: -1.27 (0.44), residues: 147 loop : -1.78 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 36 HIS 0.009 0.002 HIS B 92 PHE 0.032 0.002 PHE A 64 TYR 0.013 0.001 TYR A 80 ARG 0.009 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.431 Fit side-chains REVERT: B 90 GLN cc_start: 0.7869 (tp-100) cc_final: 0.7608 (tp40) REVERT: R 389 ASP cc_start: 0.8087 (p0) cc_final: 0.7638 (p0) REVERT: R 408 ARG cc_start: 0.8199 (ptm-80) cc_final: 0.7709 (tmm-80) REVERT: R 428 ASP cc_start: 0.8297 (p0) cc_final: 0.7939 (p0) outliers start: 11 outliers final: 10 residues processed: 63 average time/residue: 0.2155 time to fit residues: 15.8772 Evaluate side-chains 60 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 432 CYS 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: 3.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.0770 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3324 Z= 0.199 Angle : 0.730 11.066 4513 Z= 0.360 Chirality : 0.046 0.145 487 Planarity : 0.005 0.047 585 Dihedral : 4.679 21.772 458 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.86 % Favored : 92.65 % Rotamer: Outliers : 2.25 % Allowed : 20.22 % Favored : 77.53 % 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: -2.47 (0.41), residues: 408 helix: -3.71 (0.71), residues: 26 sheet: -1.14 (0.44), residues: 147 loop : -1.72 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 98 HIS 0.005 0.002 HIS B 92 PHE 0.029 0.001 PHE A 64 TYR 0.017 0.001 TYR B 50 ARG 0.011 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: B 78 ARG cc_start: 0.7825 (mmm160) cc_final: 0.7151 (mmm160) REVERT: R 389 ASP cc_start: 0.8065 (p0) cc_final: 0.7646 (p0) REVERT: R 428 ASP cc_start: 0.8336 (p0) cc_final: 0.7980 (p0) outliers start: 8 outliers final: 7 residues processed: 71 average time/residue: 0.2040 time to fit residues: 16.9898 Evaluate side-chains 62 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 432 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 3324 Z= 0.450 Angle : 0.835 12.245 4513 Z= 0.421 Chirality : 0.049 0.146 487 Planarity : 0.006 0.047 585 Dihedral : 5.311 22.719 458 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.05 % Favored : 89.46 % Rotamer: Outliers : 3.09 % Allowed : 20.79 % Favored : 76.12 % 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: -2.56 (0.40), residues: 408 helix: -4.05 (0.71), residues: 20 sheet: -1.33 (0.46), residues: 136 loop : -1.74 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 36 HIS 0.011 0.003 HIS B 92 PHE 0.037 0.002 PHE A 64 TYR 0.018 0.002 TYR B 50 ARG 0.009 0.001 ARG B 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.398 Fit side-chains REVERT: B 18 ARG cc_start: 0.7842 (mmm-85) cc_final: 0.7608 (mmm-85) REVERT: B 90 GLN cc_start: 0.7886 (tp-100) cc_final: 0.7619 (tp40) REVERT: R 389 ASP cc_start: 0.8208 (p0) cc_final: 0.7811 (p0) REVERT: R 390 LEU cc_start: 0.9252 (pp) cc_final: 0.9042 (pp) REVERT: R 408 ARG cc_start: 0.8277 (ptm-80) cc_final: 0.7829 (tmm-80) REVERT: R 428 ASP cc_start: 0.8337 (p0) cc_final: 0.7950 (p0) outliers start: 11 outliers final: 8 residues processed: 59 average time/residue: 0.2093 time to fit residues: 14.5290 Evaluate side-chains 56 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 432 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.0870 chunk 36 optimal weight: 5.9990 chunk 21 optimal weight: 0.0470 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.086338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.070309 restraints weight = 9562.509| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.40 r_work: 0.3192 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3324 Z= 0.200 Angle : 0.768 11.426 4513 Z= 0.378 Chirality : 0.047 0.145 487 Planarity : 0.005 0.049 585 Dihedral : 4.789 22.313 458 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.11 % Favored : 92.40 % Rotamer: Outliers : 2.25 % Allowed : 21.91 % Favored : 75.84 % 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: -2.39 (0.41), residues: 408 helix: -3.66 (0.74), residues: 26 sheet: -1.20 (0.45), residues: 147 loop : -1.58 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 98 HIS 0.004 0.001 HIS B 92 PHE 0.034 0.001 PHE A 64 TYR 0.022 0.001 TYR R 380 ARG 0.013 0.001 ARG B 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1366.28 seconds wall clock time: 25 minutes 19.78 seconds (1519.78 seconds total)