Starting phenix.real_space_refine on Mon Feb 10 23:20:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wck_32423/02_2025/7wck_32423.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wck_32423/02_2025/7wck_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/cci-nas-00/data/ceres_data/7wck_32423/02_2025/7wck_32423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wck_32423/02_2025/7wck_32423.map" model { file = "/net/cci-nas-00/data/ceres_data/7wck_32423/02_2025/7wck_32423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wck_32423/02_2025/7wck_32423.cif" } 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. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 3.75, per 1000 atoms: 1.16 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 - 3.00 Amino acid : True - 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: 0.83 Conformation dependent library (CDL) restraints added in 430.0 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: 0.37 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: 0.78 Time building geometry restraints manager: 0.89 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: 0.00 - 9.23: 4507 9.23 - 18.47: 5 18.47 - 27.70: 0 27.70 - 36.93: 0 36.93 - 46.16: 1 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 3.120 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 3.120 nonbonded pdb=" O PRO B 97 " pdb=" OG1 THR B 99 " model vdw 2.133 3.040 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 Time spend for trying shortcut: 0.00 ========== 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: 2.780 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.620 Find NCS groups from input model: 0.030 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.400 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.418 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: 0.2420 time to fit residues: 20.3235 Evaluate side-chains 53 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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: 0.4980 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** R 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.086812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.070923 restraints weight = 9556.347| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.42 r_work: 0.3202 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 3324 Z= 0.229 Angle : 0.715 8.330 4513 Z= 0.379 Chirality : 0.050 0.344 487 Planarity : 0.009 0.145 585 Dihedral : 5.914 41.180 458 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.84 % Favored : 91.42 % Rotamer: Outliers : 1.40 % Allowed : 10.96 % Favored : 87.64 % 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: -2.84 (0.41), residues: 408 helix: -4.17 (0.48), residues: 32 sheet: -1.36 (0.44), residues: 147 loop : -1.90 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 98 HIS 0.008 0.002 HIS B 92 PHE 0.008 0.001 PHE R 392 TYR 0.024 0.001 TYR B 50 ARG 0.004 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 73 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 ARG cc_start: 0.6891 (mmt-90) cc_final: 0.6577 (mmp80) REVERT: R 389 ASP cc_start: 0.8669 (p0) cc_final: 0.8341 (p0) outliers start: 5 outliers final: 1 residues processed: 72 average time/residue: 0.2435 time to fit residues: 20.1368 Evaluate side-chains 53 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 0.0670 chunk 33 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 ** R 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.086730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.070698 restraints weight = 9595.331| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.43 r_work: 0.3205 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3324 Z= 0.218 Angle : 0.696 6.755 4513 Z= 0.364 Chirality : 0.050 0.300 487 Planarity : 0.008 0.140 585 Dihedral : 5.509 35.309 458 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.35 % Favored : 91.91 % Rotamer: Outliers : 1.69 % Allowed : 12.36 % Favored : 85.96 % 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: -2.62 (0.41), residues: 408 helix: -3.98 (0.55), residues: 32 sheet: -1.24 (0.44), residues: 147 loop : -1.72 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 436 HIS 0.010 0.003 HIS B 92 PHE 0.015 0.001 PHE R 392 TYR 0.009 0.001 TYR R 421 ARG 0.006 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 69 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 105 LYS cc_start: 0.8629 (tppt) cc_final: 0.7803 (mtpt) REVERT: R 389 ASP cc_start: 0.8606 (p0) cc_final: 0.8404 (p0) outliers start: 6 outliers final: 2 residues processed: 69 average time/residue: 0.2340 time to fit residues: 18.5465 Evaluate side-chains 56 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain B residue 34 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 ** R 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.085560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.069253 restraints weight = 9758.133| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.49 r_work: 0.3169 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3324 Z= 0.241 Angle : 0.680 8.721 4513 Z= 0.352 Chirality : 0.049 0.281 487 Planarity : 0.007 0.140 585 Dihedral : 5.140 24.700 458 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.60 % Favored : 91.67 % Rotamer: Outliers : 2.81 % Allowed : 13.48 % Favored : 83.71 % 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: -2.54 (0.41), residues: 408 helix: -3.79 (0.60), residues: 32 sheet: -1.19 (0.44), residues: 147 loop : -1.69 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 436 HIS 0.011 0.003 HIS B 92 PHE 0.007 0.001 PHE A 29 TYR 0.012 0.001 TYR B 50 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 72 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: R 428 ASP cc_start: 0.8661 (p0) cc_final: 0.8372 (p0) outliers start: 10 outliers final: 6 residues processed: 70 average time/residue: 0.2137 time to fit residues: 17.2812 Evaluate side-chains 59 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 21 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 47 LEU 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 8 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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** ** R 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.083181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.066465 restraints weight = 9850.759| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.50 r_work: 0.3096 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3324 Z= 0.392 Angle : 0.766 8.535 4513 Z= 0.397 Chirality : 0.051 0.269 487 Planarity : 0.007 0.136 585 Dihedral : 5.373 23.958 458 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.74 % Allowed : 8.58 % Favored : 90.69 % Rotamer: Outliers : 3.37 % Allowed : 15.45 % Favored : 81.18 % 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 (0.40), residues: 408 helix: -3.51 (0.86), residues: 20 sheet: -1.49 (0.42), residues: 148 loop : -1.74 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 36 HIS 0.012 0.004 HIS B 92 PHE 0.011 0.002 PHE A 29 TYR 0.029 0.002 TYR B 50 ARG 0.005 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 68 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 95 TYR cc_start: 0.8644 (m-80) cc_final: 0.8402 (m-80) REVERT: B 18 ARG cc_start: 0.8159 (mmm-85) cc_final: 0.7697 (mmm-85) REVERT: B 90 GLN cc_start: 0.8063 (tp-100) cc_final: 0.7762 (tp-100) REVERT: B 91 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8419 (tm-30) REVERT: R 408 ARG cc_start: 0.8611 (ptm-80) cc_final: 0.8395 (ptm-80) REVERT: R 428 ASP cc_start: 0.8704 (p0) cc_final: 0.8459 (p0) outliers start: 12 outliers final: 10 residues processed: 64 average time/residue: 0.2115 time to fit residues: 15.7615 Evaluate side-chains 61 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 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 430 THR 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 27 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 0.0980 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ** R 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.085935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.069439 restraints weight = 10068.960| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.54 r_work: 0.3172 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3324 Z= 0.198 Angle : 0.726 13.833 4513 Z= 0.358 Chirality : 0.050 0.310 487 Planarity : 0.008 0.155 585 Dihedral : 4.897 22.863 458 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.74 % Allowed : 5.64 % Favored : 93.63 % Rotamer: Outliers : 2.53 % Allowed : 17.42 % Favored : 80.06 % 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: -3.52 (0.85), residues: 20 sheet: -1.37 (0.45), residues: 138 loop : -1.67 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 436 HIS 0.009 0.003 HIS B 92 PHE 0.008 0.001 PHE R 392 TYR 0.008 0.001 TYR R 423 ARG 0.007 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 73 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.396 Fit side-chains REVERT: B 18 ARG cc_start: 0.8153 (mmm-85) cc_final: 0.7670 (mmm-85) REVERT: B 105 LYS cc_start: 0.8594 (tppt) cc_final: 0.7865 (mtpt) REVERT: R 428 ASP cc_start: 0.8662 (p0) cc_final: 0.8388 (p0) outliers start: 9 outliers final: 5 residues processed: 72 average time/residue: 0.2226 time to fit residues: 18.5251 Evaluate side-chains 61 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 R residue 432 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 0.0570 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.085919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.069599 restraints weight = 9813.033| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.49 r_work: 0.3177 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2743 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= 0.207 Angle : 0.732 10.821 4513 Z= 0.373 Chirality : 0.049 0.259 487 Planarity : 0.005 0.051 585 Dihedral : 4.931 28.401 458 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.86 % Favored : 92.65 % Rotamer: Outliers : 2.25 % Allowed : 17.42 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.40), residues: 408 helix: -3.42 (0.89), residues: 20 sheet: -1.30 (0.45), residues: 138 loop : -1.56 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 436 HIS 0.011 0.003 HIS B 92 PHE 0.011 0.001 PHE B 84 TYR 0.007 0.001 TYR R 423 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 72 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.369 Fit side-chains REVERT: A 10 GLU cc_start: 0.7990 (mp0) cc_final: 0.7591 (mp0) REVERT: B 18 ARG cc_start: 0.8143 (mmm-85) cc_final: 0.7660 (mmm-85) REVERT: B 105 LYS cc_start: 0.8517 (tppt) cc_final: 0.7763 (mtpt) REVERT: R 428 ASP cc_start: 0.8677 (p0) cc_final: 0.8400 (p0) outliers start: 8 outliers final: 6 residues processed: 70 average time/residue: 0.2251 time to fit residues: 18.4693 Evaluate side-chains 67 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 14 SER Chi-restraints excluded: chain B residue 34 LEU 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 12 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 36 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 388 ASN ** R 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.085607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.069173 restraints weight = 9780.950| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.44 r_work: 0.3169 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3324 Z= 0.229 Angle : 0.741 10.649 4513 Z= 0.373 Chirality : 0.050 0.320 487 Planarity : 0.005 0.050 585 Dihedral : 4.817 23.973 458 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.11 % Favored : 92.40 % Rotamer: Outliers : 2.81 % Allowed : 17.98 % Favored : 79.21 % 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: -2.31 (0.40), residues: 408 helix: -3.27 (0.95), residues: 20 sheet: -1.32 (0.45), residues: 138 loop : -1.52 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 98 HIS 0.011 0.003 HIS B 92 PHE 0.009 0.001 PHE B 84 TYR 0.013 0.001 TYR B 50 ARG 0.009 0.000 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 74 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.406 Fit side-chains REVERT: B 18 ARG cc_start: 0.8117 (mmm-85) cc_final: 0.7814 (mmm-85) REVERT: B 75 THR cc_start: 0.6465 (m) cc_final: 0.6171 (m) REVERT: B 91 GLN cc_start: 0.8237 (tm-30) cc_final: 0.8013 (tm-30) REVERT: R 428 ASP cc_start: 0.8618 (p0) cc_final: 0.8333 (p0) outliers start: 10 outliers final: 7 residues processed: 73 average time/residue: 0.2226 time to fit residues: 18.6807 Evaluate side-chains 63 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 29 PHE 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 432 CYS Chi-restraints excluded: chain R residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.085944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.069486 restraints weight = 9906.072| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.45 r_work: 0.3175 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3324 Z= 0.239 Angle : 0.777 10.174 4513 Z= 0.394 Chirality : 0.049 0.284 487 Planarity : 0.005 0.050 585 Dihedral : 4.822 23.972 458 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.84 % Favored : 91.67 % Rotamer: Outliers : 2.25 % Allowed : 18.54 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.41), residues: 408 helix: -3.28 (0.93), residues: 20 sheet: -1.30 (0.45), residues: 138 loop : -1.44 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 98 HIS 0.010 0.003 HIS B 92 PHE 0.008 0.001 PHE B 84 TYR 0.014 0.001 TYR B 50 ARG 0.010 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 64 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.295 Fit side-chains REVERT: B 18 ARG cc_start: 0.8093 (mmm-85) cc_final: 0.7798 (mmm-85) REVERT: B 75 THR cc_start: 0.6566 (m) cc_final: 0.6238 (m) REVERT: R 428 ASP cc_start: 0.8689 (p0) cc_final: 0.8412 (p0) outliers start: 8 outliers final: 6 residues processed: 64 average time/residue: 0.2268 time to fit residues: 16.8017 Evaluate side-chains 61 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 432 CYS Chi-restraints excluded: chain R residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.086583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.070324 restraints weight = 9683.052| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.39 r_work: 0.3195 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3324 Z= 0.235 Angle : 0.815 11.351 4513 Z= 0.408 Chirality : 0.048 0.170 487 Planarity : 0.005 0.050 585 Dihedral : 4.744 23.840 458 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.11 % Favored : 92.40 % Rotamer: Outliers : 1.69 % Allowed : 19.38 % 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: -2.18 (0.41), residues: 408 helix: -3.28 (0.93), residues: 20 sheet: -1.26 (0.45), residues: 138 loop : -1.39 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 98 HIS 0.011 0.003 HIS B 92 PHE 0.006 0.001 PHE B 84 TYR 0.008 0.001 TYR R 423 ARG 0.011 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 65 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.386 Fit side-chains REVERT: B 18 ARG cc_start: 0.7973 (mmm-85) cc_final: 0.7665 (mmm-85) REVERT: B 75 THR cc_start: 0.6434 (m) cc_final: 0.6098 (m) REVERT: R 428 ASP cc_start: 0.8629 (p0) cc_final: 0.8353 (p0) outliers start: 6 outliers final: 6 residues processed: 65 average time/residue: 0.2301 time to fit residues: 17.3616 Evaluate side-chains 63 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 432 CYS Chi-restraints excluded: chain R residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 0.0570 chunk 14 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 0.0060 chunk 11 optimal weight: 0.7980 overall best weight: 0.4714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.087391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.071168 restraints weight = 9665.496| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.44 r_work: 0.3219 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3324 Z= 0.215 Angle : 0.781 10.114 4513 Z= 0.393 Chirality : 0.048 0.188 487 Planarity : 0.005 0.050 585 Dihedral : 4.649 23.816 458 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.86 % Favored : 92.65 % Rotamer: Outliers : 1.97 % Allowed : 19.66 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.41), residues: 408 helix: -3.17 (0.84), residues: 26 sheet: -1.12 (0.46), residues: 135 loop : -1.38 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 98 HIS 0.010 0.003 HIS B 92 PHE 0.034 0.001 PHE A 64 TYR 0.013 0.001 TYR B 50 ARG 0.012 0.001 ARG B 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2060.01 seconds wall clock time: 37 minutes 9.65 seconds (2229.65 seconds total)