Starting phenix.real_space_refine on Thu Dec 7 18:48:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sib_40505/12_2023/8sib_40505.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sib_40505/12_2023/8sib_40505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sib_40505/12_2023/8sib_40505.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sib_40505/12_2023/8sib_40505.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sib_40505/12_2023/8sib_40505.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sib_40505/12_2023/8sib_40505.pdb" } resolution = 2.62 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= 0.017 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 2261 2.51 5 N 619 2.21 5 O 646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 151": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3544 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3544 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 436} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 2.41, per 1000 atoms: 0.68 Number of scatterers: 3544 At special positions: 0 Unit cell: (66.4, 94.62, 74.7, 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 646 8.00 N 619 7.00 C 2261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 44 " distance=2.04 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 36 " distance=2.04 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 44 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 695.6 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 840 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 38.5% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 Processing helix chain 'A' and resid 116 through 125 removed outlier: 3.534A pdb=" N LEU A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 167 removed outlier: 3.511A pdb=" N LEU A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 191 removed outlier: 4.447A pdb=" N HIS A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 258 through 273 removed outlier: 4.302A pdb=" N LEU A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.755A pdb=" N GLN A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 331 removed outlier: 3.624A pdb=" N GLN A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.832A pdb=" N THR A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 372 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 390 through 398 removed outlier: 3.538A pdb=" N ALA A 394 " --> pdb=" O ASP A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 418 Processing helix chain 'A' and resid 419 through 426 removed outlier: 3.943A pdb=" N ALA A 423 " --> pdb=" O ARG A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 449 removed outlier: 3.507A pdb=" N LEU A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.823A pdb=" N GLU A 15 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 94 removed outlier: 6.479A pdb=" N LYS A 107 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU A 247 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL A 109 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ASP A 249 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU A 111 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR A 201 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE A 246 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY A 203 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A 248 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA A 205 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N CYS A 200 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 135 " --> pdb=" O TRP A 170 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU A 172 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE A 137 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 312 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N PHE A 381 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 314 " --> pdb=" O PHE A 381 " (cutoff:3.500A) 117 hydrogen bonds defined for protein. 342 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: 0.84 Time building geometry restraints manager: 1.33 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: 1156 1.34 - 1.47: 780 1.47 - 1.59: 1652 1.59 - 1.71: 0 1.71 - 1.83: 26 Bond restraints: 3614 Sorted by residual: bond pdb=" C GLU A 343 " pdb=" N PRO A 344 " ideal model delta sigma weight residual 1.336 1.370 -0.034 1.25e-02 6.40e+03 7.38e+00 bond pdb=" N SER A 101 " pdb=" CA SER A 101 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.16e+00 bond pdb=" C LEU A 30 " pdb=" N PRO A 31 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.04e+00 bond pdb=" C SER A 307 " pdb=" N PRO A 308 " ideal model delta sigma weight residual 1.329 1.353 -0.024 1.18e-02 7.18e+03 4.02e+00 bond pdb=" CB ILE A 412 " pdb=" CG2 ILE A 412 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.36e+00 ... (remaining 3609 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.42: 108 106.42 - 113.30: 2007 113.30 - 120.18: 1265 120.18 - 127.07: 1458 127.07 - 133.95: 58 Bond angle restraints: 4896 Sorted by residual: angle pdb=" C ARG A 46 " pdb=" N LEU A 47 " pdb=" CA LEU A 47 " ideal model delta sigma weight residual 121.54 133.47 -11.93 1.91e+00 2.74e-01 3.90e+01 angle pdb=" C GLU A 76 " pdb=" N GLU A 77 " pdb=" CA GLU A 77 " ideal model delta sigma weight residual 122.46 129.98 -7.52 1.41e+00 5.03e-01 2.84e+01 angle pdb=" C CYS A 36 " pdb=" N GLN A 37 " pdb=" CA GLN A 37 " ideal model delta sigma weight residual 121.54 131.32 -9.78 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C VAL A 48 " pdb=" N LYS A 49 " pdb=" CA LYS A 49 " ideal model delta sigma weight residual 121.54 130.64 -9.10 1.91e+00 2.74e-01 2.27e+01 angle pdb=" C GLY A 100 " pdb=" N SER A 101 " pdb=" CA SER A 101 " ideal model delta sigma weight residual 121.54 130.39 -8.85 1.91e+00 2.74e-01 2.15e+01 ... (remaining 4891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 2018 15.41 - 30.83: 117 30.83 - 46.24: 29 46.24 - 61.66: 8 61.66 - 77.07: 7 Dihedral angle restraints: 2179 sinusoidal: 877 harmonic: 1302 Sorted by residual: dihedral pdb=" CA SER A 307 " pdb=" C SER A 307 " pdb=" N PRO A 308 " pdb=" CA PRO A 308 " ideal model delta harmonic sigma weight residual -180.00 -123.29 -56.71 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA LEU A 30 " pdb=" C LEU A 30 " pdb=" N PRO A 31 " pdb=" CA PRO A 31 " ideal model delta harmonic sigma weight residual -180.00 -126.99 -53.01 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA ILE A 383 " pdb=" C ILE A 383 " pdb=" N GLY A 384 " pdb=" CA GLY A 384 " ideal model delta harmonic sigma weight residual -180.00 -131.62 -48.38 0 5.00e+00 4.00e-02 9.36e+01 ... (remaining 2176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 438 0.065 - 0.130: 103 0.130 - 0.195: 19 0.195 - 0.260: 1 0.260 - 0.325: 5 Chirality restraints: 566 Sorted by residual: chirality pdb=" CB VAL A 176 " pdb=" CA VAL A 176 " pdb=" CG1 VAL A 176 " pdb=" CG2 VAL A 176 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CG LEU A 47 " pdb=" CB LEU A 47 " pdb=" CD1 LEU A 47 " pdb=" CD2 LEU A 47 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE A 383 " pdb=" CA ILE A 383 " pdb=" CG1 ILE A 383 " pdb=" CG2 ILE A 383 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 563 not shown) Planarity restraints: 622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 95 " 0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ILE A 95 " -0.062 2.00e-02 2.50e+03 pdb=" O ILE A 95 " 0.023 2.00e-02 2.50e+03 pdb=" N ASN A 96 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 30 " -0.058 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO A 31 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 31 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C PRO A 31 " 0.055 2.00e-02 2.50e+03 pdb=" O PRO A 31 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY A 32 " -0.018 2.00e-02 2.50e+03 ... (remaining 619 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 836 2.79 - 3.32: 3127 3.32 - 3.85: 5541 3.85 - 4.37: 6449 4.37 - 4.90: 11243 Nonbonded interactions: 27196 Sorted by model distance: nonbonded pdb=" O PHE A 290 " pdb=" OG1 THR A 318 " model vdw 2.265 2.440 nonbonded pdb=" O ALA A 163 " pdb=" OG1 THR A 167 " model vdw 2.324 2.440 nonbonded pdb=" OH TYR A 108 " pdb=" O LEU A 216 " model vdw 2.338 2.440 nonbonded pdb=" NH1 ARG A 41 " pdb=" O ARG A 46 " model vdw 2.348 2.520 nonbonded pdb=" N LEU A 30 " pdb=" O LEU A 30 " model vdw 2.374 2.496 ... (remaining 27191 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: 1.330 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: 0.000 Extract box with map and model: 5.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.130 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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 : 0.007 0.060 3614 Z= 0.439 Angle : 1.304 13.305 4896 Z= 0.754 Chirality : 0.064 0.325 566 Planarity : 0.008 0.088 622 Dihedral : 11.699 75.711 1330 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 1.33 % Allowed : 12.89 % Favored : 85.78 % Rotamer: Outliers : 0.78 % Allowed : 3.88 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 17.65 % Twisted General : 0.92 % 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: -5.28 (0.28), residues: 450 helix: -4.12 (0.18), residues: 167 sheet: -1.75 (0.55), residues: 62 loop : -3.55 (0.33), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 6 HIS 0.012 0.002 HIS A 242 PHE 0.021 0.004 PHE A 381 TYR 0.028 0.003 TYR A 108 ARG 0.007 0.001 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.427 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 80 average time/residue: 1.3047 time to fit residues: 107.3200 Evaluate side-chains 41 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.411 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 86 GLN A 144 GLN A 154 GLN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 HIS A 404 ASN A 432 GLN A 461 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3614 Z= 0.234 Angle : 0.795 10.889 4896 Z= 0.405 Chirality : 0.047 0.246 566 Planarity : 0.006 0.076 622 Dihedral : 7.396 38.852 481 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.89 % Allowed : 14.00 % Favored : 85.11 % Rotamer: Outliers : 3.88 % Allowed : 12.40 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.69 % 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: -3.60 (0.33), residues: 450 helix: -1.48 (0.34), residues: 178 sheet: -2.00 (0.61), residues: 49 loop : -3.33 (0.34), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 6 HIS 0.006 0.001 HIS A 51 PHE 0.009 0.001 PHE A 146 TYR 0.009 0.001 TYR A 327 ARG 0.007 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 49 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 3 residues processed: 61 average time/residue: 1.1301 time to fit residues: 71.3233 Evaluate side-chains 39 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.5839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.3980 chunk 34 optimal weight: 0.0040 chunk 27 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 0.0870 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.0770 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.2328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3614 Z= 0.200 Angle : 0.791 15.163 4896 Z= 0.394 Chirality : 0.045 0.184 566 Planarity : 0.004 0.038 622 Dihedral : 6.996 45.909 481 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.89 % Allowed : 13.11 % Favored : 86.00 % Rotamer: Outliers : 3.10 % Allowed : 14.73 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % Twisted General : 0.46 % 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: -2.50 (0.37), residues: 450 helix: -0.12 (0.39), residues: 178 sheet: -1.35 (0.58), residues: 59 loop : -3.22 (0.37), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 6 HIS 0.007 0.001 HIS A 51 PHE 0.006 0.001 PHE A 356 TYR 0.010 0.001 TYR A 327 ARG 0.005 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 43 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 53 average time/residue: 1.0507 time to fit residues: 57.8582 Evaluate side-chains 43 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.450 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.6118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3614 Z= 0.284 Angle : 0.787 16.046 4896 Z= 0.389 Chirality : 0.048 0.238 566 Planarity : 0.004 0.040 622 Dihedral : 6.912 45.186 481 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.89 % Allowed : 14.00 % Favored : 85.11 % Rotamer: Outliers : 5.17 % Allowed : 16.02 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % Twisted General : 0.46 % 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: -2.21 (0.38), residues: 450 helix: 0.31 (0.40), residues: 177 sheet: -1.33 (0.59), residues: 59 loop : -3.20 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 207 HIS 0.005 0.001 HIS A 51 PHE 0.016 0.002 PHE A 356 TYR 0.008 0.001 TYR A 256 ARG 0.004 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 40 time to evaluate : 0.461 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 57 average time/residue: 1.0361 time to fit residues: 61.4741 Evaluate side-chains 45 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.430 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.6308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 154 GLN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3614 Z= 0.302 Angle : 0.806 16.615 4896 Z= 0.394 Chirality : 0.047 0.224 566 Planarity : 0.005 0.085 622 Dihedral : 6.868 43.729 481 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.67 % Allowed : 13.56 % Favored : 85.78 % Rotamer: Outliers : 4.13 % Allowed : 17.83 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.46 % 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: -2.00 (0.39), residues: 450 helix: 0.46 (0.41), residues: 179 sheet: -1.40 (0.66), residues: 49 loop : -2.97 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 207 HIS 0.006 0.001 HIS A 51 PHE 0.022 0.002 PHE A 356 TYR 0.014 0.002 TYR A 92 ARG 0.003 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 38 time to evaluate : 0.430 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 50 average time/residue: 1.1630 time to fit residues: 60.4750 Evaluate side-chains 40 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.432 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 0.5182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 36 optimal weight: 0.0170 chunk 20 optimal weight: 0.0670 chunk 3 optimal weight: 0.3980 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 154 GLN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3614 Z= 0.188 Angle : 0.755 17.925 4896 Z= 0.369 Chirality : 0.046 0.195 566 Planarity : 0.005 0.071 622 Dihedral : 6.547 43.505 481 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.33 % Favored : 86.44 % Rotamer: Outliers : 3.88 % Allowed : 19.38 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.46 % 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: -1.80 (0.39), residues: 450 helix: 0.63 (0.41), residues: 179 sheet: -1.28 (0.68), residues: 49 loop : -2.85 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 207 HIS 0.003 0.001 HIS A 191 PHE 0.016 0.001 PHE A 356 TYR 0.016 0.001 TYR A 92 ARG 0.002 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 39 time to evaluate : 0.426 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 52 average time/residue: 1.0375 time to fit residues: 56.0834 Evaluate side-chains 41 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.411 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 0.5924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 154 GLN A 239 ASN A 358 GLN A 461 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3614 Z= 0.280 Angle : 0.806 18.274 4896 Z= 0.390 Chirality : 0.047 0.187 566 Planarity : 0.005 0.067 622 Dihedral : 6.565 43.926 481 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.22 % Allowed : 14.67 % Favored : 85.11 % Rotamer: Outliers : 4.13 % Allowed : 20.41 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.46 % 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: -1.84 (0.39), residues: 450 helix: 0.58 (0.40), residues: 179 sheet: -1.26 (0.68), residues: 49 loop : -2.89 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 207 HIS 0.004 0.001 HIS A 191 PHE 0.017 0.001 PHE A 356 TYR 0.011 0.001 TYR A 327 ARG 0.002 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 38 time to evaluate : 0.444 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 51 average time/residue: 1.0242 time to fit residues: 54.4499 Evaluate side-chains 45 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 35 time to evaluate : 0.444 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 1.4541 time to fit residues: 2.0397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 0.0050 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3614 Z= 0.231 Angle : 0.783 18.705 4896 Z= 0.377 Chirality : 0.046 0.169 566 Planarity : 0.004 0.058 622 Dihedral : 6.475 44.096 481 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.33 % Favored : 86.44 % Rotamer: Outliers : 3.10 % Allowed : 21.71 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: -1.78 (0.39), residues: 450 helix: 0.66 (0.41), residues: 179 sheet: -1.26 (0.67), residues: 49 loop : -2.87 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 207 HIS 0.004 0.001 HIS A 191 PHE 0.015 0.001 PHE A 356 TYR 0.019 0.002 TYR A 92 ARG 0.002 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 37 time to evaluate : 0.391 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 48 average time/residue: 0.9973 time to fit residues: 49.8718 Evaluate side-chains 43 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.428 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 0.5775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3614 Z= 0.257 Angle : 0.812 19.518 4896 Z= 0.390 Chirality : 0.047 0.254 566 Planarity : 0.004 0.056 622 Dihedral : 6.459 44.406 481 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 14.44 % Favored : 85.33 % Rotamer: Outliers : 3.10 % Allowed : 22.22 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: -1.76 (0.39), residues: 450 helix: 0.70 (0.41), residues: 179 sheet: -1.28 (0.66), residues: 49 loop : -2.86 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 207 HIS 0.004 0.001 HIS A 191 PHE 0.016 0.001 PHE A 356 TYR 0.017 0.002 TYR A 92 ARG 0.002 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 34 time to evaluate : 0.473 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 45 average time/residue: 1.0330 time to fit residues: 48.5498 Evaluate side-chains 41 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.415 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.5844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 28 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 0.0050 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 overall best weight: 0.2970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3614 Z= 0.190 Angle : 0.792 20.373 4896 Z= 0.381 Chirality : 0.047 0.263 566 Planarity : 0.004 0.047 622 Dihedral : 6.212 44.324 481 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.33 % Favored : 86.44 % Rotamer: Outliers : 2.33 % Allowed : 22.48 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: -1.55 (0.40), residues: 450 helix: 0.88 (0.41), residues: 179 sheet: -1.02 (0.69), residues: 49 loop : -2.79 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 6 HIS 0.005 0.001 HIS A 149 PHE 0.014 0.001 PHE A 356 TYR 0.018 0.002 TYR A 92 ARG 0.002 0.000 ARG A 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.326 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 51 average time/residue: 0.9539 time to fit residues: 50.7551 Evaluate side-chains 45 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.397 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.6024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 24 optimal weight: 0.2980 chunk 30 optimal weight: 0.2980 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 0.0370 chunk 27 optimal weight: 0.6980 overall best weight: 0.3058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN ** A 239 ASN ** 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 = 0.3922 r_free = 0.3922 target = 0.133409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.104868 restraints weight = 6554.664| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.77 r_work: 0.3397 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3614 Z= 0.200 Angle : 0.810 20.291 4896 Z= 0.394 Chirality : 0.047 0.258 566 Planarity : 0.004 0.036 622 Dihedral : 6.019 43.182 481 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.33 % Favored : 86.44 % Rotamer: Outliers : 2.33 % Allowed : 22.74 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.48 (0.40), residues: 450 helix: 0.95 (0.41), residues: 179 sheet: -0.94 (0.69), residues: 49 loop : -2.77 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 6 HIS 0.005 0.001 HIS A 149 PHE 0.014 0.001 PHE A 356 TYR 0.017 0.002 TYR A 92 ARG 0.002 0.000 ARG A 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1760.26 seconds wall clock time: 32 minutes 1.85 seconds (1921.85 seconds total)