Starting phenix.real_space_refine on Mon May 6 16:30:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcs_38253/05_2024/8xcs_38253_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcs_38253/05_2024/8xcs_38253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcs_38253/05_2024/8xcs_38253.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcs_38253/05_2024/8xcs_38253.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcs_38253/05_2024/8xcs_38253_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcs_38253/05_2024/8xcs_38253_updated.pdb" } resolution = 2.63 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= 0.002 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2121 2.51 5 N 567 2.21 5 O 655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 371": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 3360 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3281 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 397} Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 79 Unusual residues: {'AKG': 1, 'NDP': 1, 'NH4': 1} Classifications: {'undetermined': 3, 'water': 20} Link IDs: {None: 22} Time building chain proxies: 2.47, per 1000 atoms: 0.74 Number of scatterers: 3360 At special positions: 0 Unit cell: (71.44, 69.184, 68.432, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 3 15.00 O 655 8.00 N 567 7.00 C 2121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 731.2 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 4 sheets defined 47.8% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 4.551A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 80 through 96 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 117 through 134 removed outlier: 5.690A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 340 through 343 No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 366 through 391 Processing helix chain 'A' and resid 395 through 414 removed outlier: 3.762A pdb=" N SER A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.623A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY A 104 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 74 removed outlier: 6.799A pdb=" N GLY A 106 " --> pdb=" O ARG A 73 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.180A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.807A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 162 hydrogen bonds defined for protein. 471 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: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1004 1.34 - 1.45: 483 1.45 - 1.57: 1899 1.57 - 1.69: 2 1.69 - 1.81: 27 Bond restraints: 3415 Sorted by residual: bond pdb=" O1N NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.477 1.550 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" O2B NDP A 501 " pdb=" P2B NDP A 501 " ideal model delta sigma weight residual 1.833 1.566 0.267 3.80e-02 6.93e+02 4.94e+01 bond pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.757 1.559 0.198 3.50e-02 8.16e+02 3.22e+01 bond pdb=" C1 AKG A 502 " pdb=" C2 AKG A 502 " ideal model delta sigma weight residual 1.559 1.461 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C6A NDP A 501 " pdb=" N1A NDP A 501 " ideal model delta sigma weight residual 1.368 1.253 0.115 2.90e-02 1.19e+03 1.58e+01 ... (remaining 3410 not shown) Histogram of bond angle deviations from ideal: 95.97 - 103.58: 57 103.58 - 111.20: 1368 111.20 - 118.81: 1395 118.81 - 126.42: 1742 126.42 - 134.03: 76 Bond angle restraints: 4638 Sorted by residual: angle pdb=" C1D NDP A 501 " pdb=" O4D NDP A 501 " pdb=" C4D NDP A 501 " ideal model delta sigma weight residual 105.41 127.53 -22.12 2.71e+00 1.37e-01 6.68e+01 angle pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " ideal model delta sigma weight residual 103.84 119.24 -15.40 1.91e+00 2.73e-01 6.47e+01 angle pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 107.74 122.52 -14.78 1.95e+00 2.62e-01 5.72e+01 angle pdb=" O1X NDP A 501 " pdb=" P2B NDP A 501 " pdb=" O3X NDP A 501 " ideal model delta sigma weight residual 117.46 109.42 8.04 1.17e+00 7.36e-01 4.75e+01 angle pdb=" O2X NDP A 501 " pdb=" P2B NDP A 501 " pdb=" O3X NDP A 501 " ideal model delta sigma weight residual 117.33 108.86 8.47 1.48e+00 4.57e-01 3.28e+01 ... (remaining 4633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.95: 1931 30.95 - 61.89: 84 61.89 - 92.84: 7 92.84 - 123.78: 0 123.78 - 154.73: 1 Dihedral angle restraints: 2023 sinusoidal: 828 harmonic: 1195 Sorted by residual: dihedral pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " ideal model delta sinusoidal sigma weight residual 175.04 20.31 154.73 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CB LYS A 304 " pdb=" CG LYS A 304 " pdb=" CD LYS A 304 " pdb=" CE LYS A 304 " ideal model delta sinusoidal sigma weight residual 180.00 121.19 58.81 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 2020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 443 0.079 - 0.159: 52 0.159 - 0.238: 3 0.238 - 0.318: 3 0.318 - 0.397: 3 Chirality restraints: 504 Sorted by residual: chirality pdb=" C4D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" C5D NDP A 501 " pdb=" O4D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.32 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" C2D NDP A 501 " pdb=" C1D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" O2D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.34 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C1B NDP A 501 " pdb=" C2B NDP A 501 " pdb=" N9A NDP A 501 " pdb=" O4B NDP A 501 " both_signs ideal model delta sigma weight residual False 2.59 2.24 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 501 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 501 " -0.139 2.00e-02 2.50e+03 8.17e-02 8.34e+01 pdb=" C3N NDP A 501 " 0.008 2.00e-02 2.50e+03 pdb=" C4N NDP A 501 " -0.026 2.00e-02 2.50e+03 pdb=" C7N NDP A 501 " 0.058 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 501 " -0.035 2.00e-02 2.50e+03 6.15e-02 3.78e+01 pdb=" C5N NDP A 501 " 0.078 2.00e-02 2.50e+03 pdb=" C6N NDP A 501 " -0.080 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 394 " 0.021 2.00e-02 2.50e+03 4.08e-02 1.66e+01 pdb=" C HIS A 394 " -0.071 2.00e-02 2.50e+03 pdb=" O HIS A 394 " 0.026 2.00e-02 2.50e+03 pdb=" N MET A 395 " 0.024 2.00e-02 2.50e+03 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 1274 2.88 - 3.39: 3308 3.39 - 3.89: 6116 3.89 - 4.40: 7240 4.40 - 4.90: 11656 Nonbonded interactions: 29594 Sorted by model distance: nonbonded pdb=" O HIS A 61 " pdb=" O HOH A 601 " model vdw 2.381 2.440 nonbonded pdb=" O ASP A 145 " pdb=" O HOH A 602 " model vdw 2.445 2.440 nonbonded pdb=" O VAL A 317 " pdb=" ND2 ASN A 344 " model vdw 2.448 2.520 nonbonded pdb=" O ARG A 65 " pdb=" O HOH A 603 " model vdw 2.461 2.440 nonbonded pdb=" O THR A 148 " pdb=" O HOH A 602 " model vdw 2.469 2.440 ... (remaining 29589 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 3.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.490 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.267 3415 Z= 0.666 Angle : 1.096 22.116 4638 Z= 0.584 Chirality : 0.059 0.397 504 Planarity : 0.006 0.082 592 Dihedral : 16.414 154.727 1261 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.69 % Allowed : 3.52 % Favored : 91.79 % 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: 0.58 (0.43), residues: 416 helix: 0.93 (0.36), residues: 210 sheet: 0.54 (0.74), residues: 60 loop : -0.33 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.398 Fit side-chains REVERT: A 12 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8074 (mptt) outliers start: 16 outliers final: 2 residues processed: 76 average time/residue: 1.6084 time to fit residues: 124.9619 Evaluate side-chains 49 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3415 Z= 0.310 Angle : 0.546 7.063 4638 Z= 0.289 Chirality : 0.045 0.142 504 Planarity : 0.005 0.047 592 Dihedral : 11.056 163.754 477 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.93 % Allowed : 11.44 % Favored : 85.63 % 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: 1.01 (0.43), residues: 416 helix: 1.57 (0.36), residues: 211 sheet: 0.13 (0.69), residues: 61 loop : -0.35 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 364 HIS 0.005 0.001 HIS A 388 PHE 0.017 0.002 PHE A 341 TYR 0.014 0.002 TYR A 363 ARG 0.002 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.350 Fit side-chains REVERT: A 12 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8272 (mttp) REVERT: A 113 LYS cc_start: 0.8728 (mttp) cc_final: 0.8435 (mtpt) REVERT: A 229 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8525 (tttp) REVERT: A 371 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7331 (pt0) outliers start: 10 outliers final: 1 residues processed: 50 average time/residue: 1.7334 time to fit residues: 88.7469 Evaluate side-chains 44 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 0.3980 chunk 25 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3415 Z= 0.255 Angle : 0.500 4.411 4638 Z= 0.264 Chirality : 0.043 0.137 504 Planarity : 0.004 0.050 592 Dihedral : 10.281 162.092 474 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.35 % Allowed : 11.44 % Favored : 86.22 % 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: 1.12 (0.43), residues: 416 helix: 1.69 (0.36), residues: 211 sheet: 0.09 (0.68), residues: 61 loop : -0.31 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 30 HIS 0.004 0.001 HIS A 388 PHE 0.015 0.002 PHE A 341 TYR 0.013 0.001 TYR A 363 ARG 0.001 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.408 Fit side-chains REVERT: A 113 LYS cc_start: 0.8721 (mttp) cc_final: 0.8425 (mtpt) REVERT: A 246 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7405 (mtt180) REVERT: A 371 GLU cc_start: 0.7621 (pt0) cc_final: 0.7356 (pt0) outliers start: 8 outliers final: 3 residues processed: 49 average time/residue: 1.6706 time to fit residues: 83.8855 Evaluate side-chains 44 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.3980 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 0.0570 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3415 Z= 0.159 Angle : 0.461 5.029 4638 Z= 0.242 Chirality : 0.041 0.130 504 Planarity : 0.004 0.050 592 Dihedral : 9.571 162.116 470 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.35 % Allowed : 12.90 % Favored : 84.75 % 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: 1.31 (0.43), residues: 416 helix: 1.87 (0.36), residues: 211 sheet: 0.18 (0.69), residues: 61 loop : -0.27 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 30 HIS 0.003 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.410 Fit side-chains REVERT: A 113 LYS cc_start: 0.8714 (mttp) cc_final: 0.8381 (mtpt) REVERT: A 246 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7383 (mtt180) REVERT: A 371 GLU cc_start: 0.7605 (pt0) cc_final: 0.7391 (pt0) outliers start: 8 outliers final: 1 residues processed: 51 average time/residue: 1.6608 time to fit residues: 86.7263 Evaluate side-chains 46 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3415 Z= 0.180 Angle : 0.458 4.329 4638 Z= 0.241 Chirality : 0.042 0.129 504 Planarity : 0.004 0.050 592 Dihedral : 9.337 159.876 470 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.93 % Allowed : 12.02 % Favored : 85.04 % 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: 1.34 (0.43), residues: 416 helix: 1.90 (0.36), residues: 211 sheet: 0.19 (0.69), residues: 61 loop : -0.25 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 30 HIS 0.003 0.001 HIS A 388 PHE 0.012 0.001 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.384 Fit side-chains REVERT: A 113 LYS cc_start: 0.8720 (mttp) cc_final: 0.8385 (mtpt) REVERT: A 246 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7302 (mtt180) outliers start: 10 outliers final: 1 residues processed: 52 average time/residue: 1.5362 time to fit residues: 82.0370 Evaluate side-chains 47 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 18 optimal weight: 0.0970 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3415 Z= 0.196 Angle : 0.468 4.398 4638 Z= 0.247 Chirality : 0.042 0.131 504 Planarity : 0.004 0.050 592 Dihedral : 9.179 155.892 470 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.52 % Allowed : 11.14 % Favored : 85.34 % 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: 1.39 (0.43), residues: 416 helix: 1.93 (0.36), residues: 210 sheet: 0.43 (0.70), residues: 59 loop : -0.31 (0.56), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 HIS 0.004 0.001 HIS A 388 PHE 0.012 0.001 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.404 Fit side-chains REVERT: A 113 LYS cc_start: 0.8726 (mttp) cc_final: 0.8387 (mtpt) REVERT: A 229 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8457 (tttp) REVERT: A 246 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7324 (mtt180) outliers start: 12 outliers final: 4 residues processed: 54 average time/residue: 1.5858 time to fit residues: 87.8462 Evaluate side-chains 52 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3415 Z= 0.429 Angle : 0.570 5.098 4638 Z= 0.304 Chirality : 0.048 0.145 504 Planarity : 0.005 0.055 592 Dihedral : 9.695 150.300 470 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.93 % Allowed : 11.73 % Favored : 85.34 % 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: 1.01 (0.42), residues: 416 helix: 1.61 (0.35), residues: 211 sheet: 0.29 (0.70), residues: 59 loop : -0.49 (0.55), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 364 HIS 0.007 0.002 HIS A 388 PHE 0.022 0.002 PHE A 341 TYR 0.018 0.002 TYR A 363 ARG 0.002 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.396 Fit side-chains REVERT: A 229 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8538 (tttp) REVERT: A 246 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7367 (mtt180) outliers start: 10 outliers final: 3 residues processed: 49 average time/residue: 1.6913 time to fit residues: 84.8587 Evaluate side-chains 45 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3415 Z= 0.180 Angle : 0.473 5.016 4638 Z= 0.249 Chirality : 0.042 0.131 504 Planarity : 0.004 0.052 592 Dihedral : 9.313 148.029 470 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.47 % Allowed : 14.66 % Favored : 83.87 % 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: 1.25 (0.43), residues: 416 helix: 1.82 (0.36), residues: 211 sheet: 0.39 (0.70), residues: 59 loop : -0.40 (0.55), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 30 HIS 0.004 0.001 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.012 0.001 TYR A 363 ARG 0.001 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.396 Fit side-chains REVERT: A 246 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7335 (mtt180) outliers start: 5 outliers final: 3 residues processed: 45 average time/residue: 1.8540 time to fit residues: 85.4583 Evaluate side-chains 45 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3415 Z= 0.147 Angle : 0.445 5.116 4638 Z= 0.232 Chirality : 0.041 0.125 504 Planarity : 0.004 0.049 592 Dihedral : 8.678 144.429 470 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.47 % Allowed : 14.66 % Favored : 83.87 % 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: 1.45 (0.43), residues: 416 helix: 2.04 (0.36), residues: 210 sheet: 0.23 (0.69), residues: 61 loop : -0.26 (0.57), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 30 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.416 Fit side-chains REVERT: A 12 LYS cc_start: 0.8557 (mttp) cc_final: 0.8357 (mttm) REVERT: A 246 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7302 (mtt180) REVERT: A 388 HIS cc_start: 0.8964 (OUTLIER) cc_final: 0.8357 (t70) outliers start: 5 outliers final: 1 residues processed: 51 average time/residue: 1.7182 time to fit residues: 89.7466 Evaluate side-chains 47 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 0.0370 chunk 6 optimal weight: 2.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3415 Z= 0.158 Angle : 0.456 5.408 4638 Z= 0.238 Chirality : 0.041 0.128 504 Planarity : 0.004 0.050 592 Dihedral : 8.445 141.485 470 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.17 % Allowed : 14.08 % Favored : 84.75 % 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: 1.51 (0.43), residues: 416 helix: 2.07 (0.36), residues: 210 sheet: 0.28 (0.70), residues: 61 loop : -0.21 (0.57), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.000 0.000 ARG A 265 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.384 Fit side-chains REVERT: A 12 LYS cc_start: 0.8559 (mttp) cc_final: 0.8359 (mttm) REVERT: A 246 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7256 (mtt180) REVERT: A 388 HIS cc_start: 0.9006 (OUTLIER) cc_final: 0.8343 (t70) outliers start: 4 outliers final: 1 residues processed: 47 average time/residue: 1.7205 time to fit residues: 82.7796 Evaluate side-chains 46 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.103231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.077823 restraints weight = 4330.931| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 1.44 r_work: 0.2624 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3415 Z= 0.288 Angle : 0.517 6.308 4638 Z= 0.272 Chirality : 0.044 0.131 504 Planarity : 0.005 0.054 592 Dihedral : 9.032 144.446 470 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.17 % Allowed : 13.78 % Favored : 85.04 % 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: 1.28 (0.43), residues: 416 helix: 1.84 (0.36), residues: 210 sheet: 0.37 (0.70), residues: 59 loop : -0.34 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.005 0.001 HIS A 388 PHE 0.017 0.002 PHE A 341 TYR 0.014 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1870.92 seconds wall clock time: 33 minutes 58.45 seconds (2038.45 seconds total)