Starting phenix.real_space_refine on Wed Jun 4 14:26:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wck_32423/06_2025/7wck_32423.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wck_32423/06_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_32423/06_2025/7wck_32423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wck_32423/06_2025/7wck_32423.map" model { file = "/net/cci-nas-00/data/ceres_data/7wck_32423/06_2025/7wck_32423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wck_32423/06_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-5710/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: 3.98, per 1000 atoms: 1.23 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: 0.73 Conformation dependent library (CDL) restraints added in 384.1 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: 0.46 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: 0.90 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: 5.390 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.230 Find NCS groups from input model: 0.040 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.840 ------------------------------------------------------------------------------- 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 3331 Z= 0.473 Angle : 1.354 46.164 4527 Z= 0.653 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 Details of bonding type rmsd hydrogen bonds : bond 0.25429 ( 73) hydrogen bonds : angle 10.66469 ( 198) SS BOND : bond 0.01076 ( 7) SS BOND : angle 2.41355 ( 14) covalent geometry : bond 0.00810 ( 3324) covalent geometry : angle 1.34961 ( 4513) *********************** 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 : 0.394 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: 0.2304 time to fit residues: 19.3813 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 : 0.403 ------------------------------------------------------------------------------- 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): 0.3366 rms_B_bonded: 3.42 r_work: 0.3204 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 3331 Z= 0.152 Angle : 0.716 8.330 4527 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 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 73) hydrogen bonds : angle 6.92723 ( 198) SS BOND : bond 0.00472 ( 7) SS BOND : angle 1.09944 ( 14) covalent geometry : bond 0.00344 ( 3324) covalent geometry : angle 0.71465 ( 4513) *********************** 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 : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 ARG cc_start: 0.6898 (mmt-90) cc_final: 0.6592 (mmp80) REVERT: R 389 ASP cc_start: 0.8645 (p0) cc_final: 0.8308 (p0) outliers start: 5 outliers final: 1 residues processed: 72 average time/residue: 0.2473 time to fit residues: 20.4597 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 : 0.408 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 0.1980 chunk 29 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.087403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.071006 restraints weight = 9644.926| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.58 r_work: 0.3201 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3331 Z= 0.141 Angle : 0.694 7.010 4527 Z= 0.363 Chirality : 0.050 0.297 487 Planarity : 0.008 0.140 585 Dihedral : 5.422 33.922 458 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.74 % Allowed : 6.86 % Favored : 92.40 % Rotamer: Outliers : 1.69 % Allowed : 12.64 % Favored : 85.67 % 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: -2.60 (0.41), residues: 408 helix: -3.99 (0.55), residues: 32 sheet: -1.21 (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 0.009 0.003 HIS B 92 PHE 0.017 0.001 PHE R 392 TYR 0.007 0.001 TYR R 423 ARG 0.006 0.000 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.03074 ( 73) hydrogen bonds : angle 6.13137 ( 198) SS BOND : bond 0.00482 ( 7) SS BOND : angle 1.17740 ( 14) covalent geometry : bond 0.00321 ( 3324) covalent geometry : angle 0.69159 ( 4513) *********************** 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 71 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8301 (p0) REVERT: B 91 GLN cc_start: 0.8066 (tm130) cc_final: 0.7852 (tm-30) REVERT: B 105 LYS cc_start: 0.8615 (tppt) cc_final: 0.7752 (mtpt) outliers start: 6 outliers final: 2 residues processed: 71 average time/residue: 0.2388 time to fit residues: 19.5287 Evaluate side-chains 61 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 103 ASN 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: 1.9990 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.0000 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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** ** 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 = 0.3689 r_free = 0.3689 target = 0.086299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.070126 restraints weight = 9740.469| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.48 r_work: 0.3185 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3331 Z= 0.151 Angle : 0.670 8.648 4527 Z= 0.346 Chirality : 0.048 0.274 487 Planarity : 0.007 0.140 585 Dihedral : 5.042 22.910 458 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.11 % Favored : 92.16 % Rotamer: Outliers : 3.37 % Allowed : 13.48 % Favored : 83.15 % 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: -2.46 (0.41), residues: 408 helix: -3.82 (0.68), residues: 26 sheet: -1.20 (0.43), residues: 149 loop : -1.65 (0.40), residues: 233 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 0.006 0.001 PHE R 392 TYR 0.012 0.001 TYR B 50 ARG 0.006 0.000 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.02793 ( 73) hydrogen bonds : angle 5.99169 ( 198) SS BOND : bond 0.00413 ( 7) SS BOND : angle 1.53653 ( 14) covalent geometry : bond 0.00347 ( 3324) covalent geometry : angle 0.66506 ( 4513) *********************** 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 74 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 78 ARG cc_start: 0.7940 (mmm160) cc_final: 0.7736 (mmm160) REVERT: B 91 GLN cc_start: 0.8300 (tm130) cc_final: 0.8071 (tm-30) outliers start: 12 outliers final: 7 residues processed: 70 average time/residue: 0.2293 time to fit residues: 18.6101 Evaluate side-chains 60 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 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 21 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain R residue 430 THR 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: 5.9990 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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** ** 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 = 0.3636 r_free = 0.3636 target = 0.083472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.066684 restraints weight = 9854.114| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.49 r_work: 0.3103 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 3331 Z= 0.266 Angle : 0.760 8.478 4527 Z= 0.391 Chirality : 0.050 0.282 487 Planarity : 0.007 0.136 585 Dihedral : 5.317 23.719 458 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.74 % Allowed : 8.09 % Favored : 91.18 % Rotamer: Outliers : 3.65 % Allowed : 16.29 % 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: -2.59 (0.40), residues: 408 helix: -3.78 (0.75), residues: 20 sheet: -1.39 (0.43), residues: 148 loop : -1.75 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 36 HIS 0.013 0.003 HIS B 92 PHE 0.010 0.002 PHE A 29 TYR 0.030 0.002 TYR B 50 ARG 0.002 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 73) hydrogen bonds : angle 6.20429 ( 198) SS BOND : bond 0.00443 ( 7) SS BOND : angle 1.49367 ( 14) covalent geometry : bond 0.00602 ( 3324) covalent geometry : angle 0.75704 ( 4513) *********************** 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 70 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 95 TYR cc_start: 0.8657 (m-80) cc_final: 0.8409 (m-80) REVERT: B 18 ARG cc_start: 0.8281 (mmm-85) cc_final: 0.7775 (mmm-85) REVERT: B 78 ARG cc_start: 0.8097 (mmm160) cc_final: 0.7444 (mmm160) REVERT: B 90 GLN cc_start: 0.8005 (tp-100) cc_final: 0.7757 (tp40) REVERT: B 91 GLN cc_start: 0.8657 (tm130) cc_final: 0.8437 (tm-30) REVERT: R 389 ASP cc_start: 0.8658 (p0) cc_final: 0.8259 (p0) REVERT: R 408 ARG cc_start: 0.8604 (ptm-80) cc_final: 0.8386 (ptm-80) REVERT: R 428 ASP cc_start: 0.8672 (p0) cc_final: 0.8430 (p0) outliers start: 13 outliers final: 7 residues processed: 67 average time/residue: 0.2191 time to fit residues: 17.0965 Evaluate side-chains 60 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 47 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 432 CYS 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: 0.5980 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** ** 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 = 0.3675 r_free = 0.3675 target = 0.085417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.068828 restraints weight = 10053.936| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.53 r_work: 0.3158 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3331 Z= 0.145 Angle : 0.703 9.738 4527 Z= 0.355 Chirality : 0.049 0.261 487 Planarity : 0.007 0.136 585 Dihedral : 4.911 23.108 458 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.74 % Allowed : 6.37 % Favored : 92.89 % Rotamer: Outliers : 2.53 % Allowed : 17.13 % 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: -2.51 (0.40), residues: 408 helix: -3.71 (0.77), residues: 20 sheet: -1.38 (0.45), residues: 139 loop : -1.68 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 436 HIS 0.010 0.003 HIS B 92 PHE 0.006 0.001 PHE A 29 TYR 0.008 0.001 TYR R 423 ARG 0.002 0.000 ARG R 346 Details of bonding type rmsd hydrogen bonds : bond 0.02506 ( 73) hydrogen bonds : angle 5.88443 ( 198) SS BOND : bond 0.00446 ( 7) SS BOND : angle 1.19351 ( 14) covalent geometry : bond 0.00329 ( 3324) covalent geometry : angle 0.70083 ( 4513) *********************** 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 72 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: B 18 ARG cc_start: 0.8230 (mmm-85) cc_final: 0.7686 (mmm-85) REVERT: B 78 ARG cc_start: 0.8055 (mmm160) cc_final: 0.7338 (mmm160) REVERT: B 91 GLN cc_start: 0.8165 (tm130) cc_final: 0.7947 (tm-30) REVERT: B 105 LYS cc_start: 0.8577 (tppt) cc_final: 0.7818 (mtpt) REVERT: R 389 ASP cc_start: 0.8577 (p0) cc_final: 0.8155 (p0) REVERT: R 428 ASP cc_start: 0.8623 (p0) cc_final: 0.8335 (p0) outliers start: 9 outliers final: 5 residues processed: 71 average time/residue: 0.2237 time to fit residues: 18.3234 Evaluate side-chains 62 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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: 2.9990 chunk 4 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3682 r_free = 0.3682 target = 0.085827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.069490 restraints weight = 9801.168| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.48 r_work: 0.3173 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3331 Z= 0.138 Angle : 0.706 10.453 4527 Z= 0.360 Chirality : 0.049 0.247 487 Planarity : 0.005 0.051 585 Dihedral : 4.901 24.850 458 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.11 % Favored : 92.40 % Rotamer: Outliers : 1.97 % Allowed : 18.54 % 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: -2.45 (0.40), residues: 408 helix: -3.37 (0.80), residues: 26 sheet: -1.31 (0.45), residues: 137 loop : -1.62 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 436 HIS 0.010 0.003 HIS B 92 PHE 0.027 0.001 PHE A 64 TYR 0.024 0.001 TYR B 50 ARG 0.002 0.000 ARG R 346 Details of bonding type rmsd hydrogen bonds : bond 0.02418 ( 73) hydrogen bonds : angle 5.81808 ( 198) SS BOND : bond 0.00449 ( 7) SS BOND : angle 1.14269 ( 14) covalent geometry : bond 0.00320 ( 3324) covalent geometry : angle 0.70392 ( 4513) *********************** 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 69 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.413 Fit side-chains REVERT: A 23 LYS cc_start: 0.8788 (ttmm) cc_final: 0.8553 (mmtm) REVERT: B 18 ARG cc_start: 0.8193 (mmm-85) cc_final: 0.7698 (mmm-85) REVERT: B 78 ARG cc_start: 0.8115 (mmm160) cc_final: 0.7230 (mmm160) REVERT: B 91 GLN cc_start: 0.8173 (tm130) cc_final: 0.7931 (tm-30) REVERT: B 105 LYS cc_start: 0.8545 (tppt) cc_final: 0.7865 (mtpt) REVERT: R 389 ASP cc_start: 0.8579 (p0) cc_final: 0.8165 (p0) REVERT: R 428 ASP cc_start: 0.8683 (p0) cc_final: 0.8402 (p0) outliers start: 7 outliers final: 6 residues processed: 68 average time/residue: 0.2452 time to fit residues: 19.0306 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 : 0.415 ------------------------------------------------------------------------------- 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: 2.9990 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 30 optimal weight: 0.0670 chunk 36 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3642 r_free = 0.3642 target = 0.083844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.067014 restraints weight = 9817.862| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.47 r_work: 0.3115 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3331 Z= 0.231 Angle : 0.755 10.680 4527 Z= 0.388 Chirality : 0.048 0.194 487 Planarity : 0.005 0.050 585 Dihedral : 5.102 24.482 458 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.07 % Favored : 90.44 % Rotamer: Outliers : 1.97 % Allowed : 17.42 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.40), residues: 408 helix: -3.22 (0.95), residues: 20 sheet: -1.44 (0.44), residues: 138 loop : -1.57 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 36 HIS 0.013 0.003 HIS B 92 PHE 0.024 0.002 PHE A 64 TYR 0.013 0.002 TYR R 453 ARG 0.008 0.001 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.02854 ( 73) hydrogen bonds : angle 6.09905 ( 198) SS BOND : bond 0.00401 ( 7) SS BOND : angle 1.21575 ( 14) covalent geometry : bond 0.00526 ( 3324) covalent geometry : angle 0.75346 ( 4513) *********************** 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 69 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: B 91 GLN cc_start: 0.8492 (tm130) cc_final: 0.8254 (tm-30) REVERT: R 389 ASP cc_start: 0.8590 (p0) cc_final: 0.8199 (p0) REVERT: R 428 ASP cc_start: 0.8682 (p0) cc_final: 0.8393 (p0) outliers start: 7 outliers final: 7 residues processed: 68 average time/residue: 0.2380 time to fit residues: 18.8630 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 : 0.373 ------------------------------------------------------------------------------- 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 B residue 47 LEU 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 7 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.084087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.067269 restraints weight = 9903.890| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.46 r_work: 0.3124 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3331 Z= 0.220 Angle : 0.799 9.795 4527 Z= 0.408 Chirality : 0.048 0.188 487 Planarity : 0.005 0.050 585 Dihedral : 5.123 25.286 458 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.56 % Favored : 89.95 % Rotamer: Outliers : 2.81 % Allowed : 19.38 % Favored : 77.81 % 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: -2.37 (0.40), residues: 408 helix: -3.18 (0.93), residues: 20 sheet: -1.48 (0.44), residues: 138 loop : -1.48 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 36 HIS 0.012 0.003 HIS B 92 PHE 0.021 0.001 PHE A 64 TYR 0.026 0.002 TYR B 50 ARG 0.012 0.001 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.02931 ( 73) hydrogen bonds : angle 6.18598 ( 198) SS BOND : bond 0.00430 ( 7) SS BOND : angle 1.21380 ( 14) covalent geometry : bond 0.00507 ( 3324) covalent geometry : angle 0.79706 ( 4513) *********************** 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 69 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.352 Fit side-chains REVERT: A 23 LYS cc_start: 0.8782 (ttmm) cc_final: 0.8550 (mmtm) REVERT: B 18 ARG cc_start: 0.7914 (mmm160) cc_final: 0.7378 (mmm-85) REVERT: B 91 GLN cc_start: 0.8391 (tm130) cc_final: 0.8162 (tm-30) REVERT: R 389 ASP cc_start: 0.8557 (p0) cc_final: 0.8164 (p0) REVERT: R 428 ASP cc_start: 0.8694 (p0) cc_final: 0.8408 (p0) outliers start: 10 outliers final: 8 residues processed: 67 average time/residue: 0.2015 time to fit residues: 15.8254 Evaluate side-chains 61 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 14 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 104 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 10 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 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 38 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 = 0.3676 r_free = 0.3676 target = 0.085534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.068795 restraints weight = 9624.980| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.45 r_work: 0.3160 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3331 Z= 0.165 Angle : 0.785 8.657 4527 Z= 0.397 Chirality : 0.048 0.189 487 Planarity : 0.006 0.051 585 Dihedral : 4.900 24.485 458 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.84 % Favored : 91.67 % Rotamer: Outliers : 1.97 % Allowed : 20.22 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.41), residues: 408 helix: -3.16 (0.95), residues: 20 sheet: -1.40 (0.45), residues: 138 loop : -1.45 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 98 HIS 0.010 0.003 HIS B 92 PHE 0.020 0.001 PHE A 64 TYR 0.025 0.002 TYR B 50 ARG 0.011 0.001 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.02618 ( 73) hydrogen bonds : angle 6.30607 ( 198) SS BOND : bond 0.00356 ( 7) SS BOND : angle 1.35952 ( 14) covalent geometry : bond 0.00390 ( 3324) covalent geometry : angle 0.78290 ( 4513) ********************** 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: 7 poor density : 58 time to evaluate : 0.413 Fit side-chains REVERT: B 18 ARG cc_start: 0.7761 (mmm160) cc_final: 0.7326 (mmm-85) REVERT: B 91 GLN cc_start: 0.8140 (tm130) cc_final: 0.7815 (tm-30) REVERT: R 389 ASP cc_start: 0.8540 (p0) cc_final: 0.8168 (p0) REVERT: R 428 ASP cc_start: 0.8714 (p0) cc_final: 0.8427 (p0) outliers start: 7 outliers final: 6 residues processed: 65 average time/residue: 0.2297 time to fit residues: 17.2860 Evaluate side-chains 64 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 14 SER 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 18 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.0370 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.085055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.068484 restraints weight = 9661.547| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.46 r_work: 0.3152 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3331 Z= 0.179 Angle : 0.787 8.597 4527 Z= 0.399 Chirality : 0.048 0.185 487 Planarity : 0.005 0.050 585 Dihedral : 4.840 24.544 458 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.49 % Allowed : 8.82 % Favored : 90.69 % Rotamer: Outliers : 1.69 % Allowed : 19.66 % 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: -2.24 (0.41), residues: 408 helix: -2.95 (1.23), residues: 14 sheet: -1.43 (0.45), residues: 139 loop : -1.44 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 436 HIS 0.012 0.003 HIS B 92 PHE 0.020 0.001 PHE A 64 TYR 0.025 0.002 TYR B 50 ARG 0.011 0.001 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.02684 ( 73) hydrogen bonds : angle 6.26507 ( 198) SS BOND : bond 0.00406 ( 7) SS BOND : angle 1.32670 ( 14) covalent geometry : bond 0.00422 ( 3324) covalent geometry : angle 0.78478 ( 4513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2150.24 seconds wall clock time: 37 minutes 38.74 seconds (2258.74 seconds total)