Starting phenix.real_space_refine on Thu Dec 7 18:50:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsn_18637/12_2023/8qsn_18637.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsn_18637/12_2023/8qsn_18637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsn_18637/12_2023/8qsn_18637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsn_18637/12_2023/8qsn_18637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsn_18637/12_2023/8qsn_18637.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsn_18637/12_2023/8qsn_18637.pdb" } resolution = 3.54 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= -0.001 sd= 0.013 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 20 5.16 5 C 2377 2.51 5 N 573 2.21 5 O 609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3579 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3579 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 18, 'TRANS': 445} Chain breaks: 3 Time building chain proxies: 2.53, per 1000 atoms: 0.71 Number of scatterers: 3579 At special positions: 0 Unit cell: (80.465, 70.015, 65.835, 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 20 16.00 O 609 8.00 N 573 7.00 C 2377 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: 1.35 Conformation dependent library (CDL) restraints added in 781.7 milliseconds 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 846 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 83.4% alpha, 1.7% 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 33 through 57 removed outlier: 4.287A pdb=" N ASN A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 70 through 98 removed outlier: 3.899A pdb=" N SER A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 102 through 118 Processing helix chain 'A' and resid 156 through 183 removed outlier: 4.226A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.629A pdb=" N VAL A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.818A pdb=" N THR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 246 removed outlier: 3.931A pdb=" N GLY A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Proline residue: A 229 - end of helix removed outlier: 3.638A pdb=" N VAL A 246 " --> pdb=" O CYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 273 Processing helix chain 'A' and resid 297 through 305 removed outlier: 3.954A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY A 305 " --> pdb=" O MET A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 347 removed outlier: 3.942A pdb=" N VAL A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Proline residue: A 323 - end of helix Proline residue: A 330 - end of helix removed outlier: 3.691A pdb=" N VAL A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 349 No H-bonds generated for 'chain 'A' and resid 348 through 349' Processing helix chain 'A' and resid 365 through 366 No H-bonds generated for 'chain 'A' and resid 365 through 366' Processing helix chain 'A' and resid 367 through 396 removed outlier: 3.958A pdb=" N ASP A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) Proline residue: A 382 - end of helix removed outlier: 5.109A pdb=" N ASP A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Proline residue: A 390 - end of helix Processing helix chain 'A' and resid 400 through 431 removed outlier: 3.528A pdb=" N LYS A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 removed outlier: 4.034A pdb=" N TRP A 453 " --> pdb=" O SER A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 453' Processing helix chain 'A' and resid 454 through 468 Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 484 through 510 Processing helix chain 'A' and resid 531 through 560 removed outlier: 3.573A pdb=" N HIS A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 439 281 hydrogen bonds defined for protein. 837 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: 1.02 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1081 1.34 - 1.46: 817 1.46 - 1.58: 1743 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 3672 Sorted by residual: bond pdb=" CB PRO A 399 " pdb=" CG PRO A 399 " ideal model delta sigma weight residual 1.492 1.537 -0.045 5.00e-02 4.00e+02 8.11e-01 bond pdb=" CA ILE A 329 " pdb=" C ILE A 329 " ideal model delta sigma weight residual 1.523 1.531 -0.008 9.20e-03 1.18e+04 7.12e-01 bond pdb=" C VAL A 246 " pdb=" O VAL A 246 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 6.67e-01 bond pdb=" CB PRO A 306 " pdb=" CG PRO A 306 " ideal model delta sigma weight residual 1.492 1.524 -0.032 5.00e-02 4.00e+02 4.05e-01 bond pdb=" N VAL A 322 " pdb=" CA VAL A 322 " ideal model delta sigma weight residual 1.463 1.470 -0.007 1.18e-02 7.18e+03 4.00e-01 ... (remaining 3667 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.07: 97 107.07 - 113.80: 2051 113.80 - 120.53: 1489 120.53 - 127.26: 1307 127.26 - 133.99: 41 Bond angle restraints: 4985 Sorted by residual: angle pdb=" C PHE A 247 " pdb=" N ILE A 248 " pdb=" CA ILE A 248 " ideal model delta sigma weight residual 121.97 125.78 -3.81 1.80e+00 3.09e-01 4.48e+00 angle pdb=" N ILE A 466 " pdb=" CA ILE A 466 " pdb=" C ILE A 466 " ideal model delta sigma weight residual 113.00 110.27 2.73 1.30e+00 5.92e-01 4.42e+00 angle pdb=" N GLU A 309 " pdb=" CA GLU A 309 " pdb=" C GLU A 309 " ideal model delta sigma weight residual 110.80 115.23 -4.43 2.13e+00 2.20e-01 4.32e+00 angle pdb=" C THR A 308 " pdb=" N GLU A 309 " pdb=" CA GLU A 309 " ideal model delta sigma weight residual 121.54 125.26 -3.72 1.91e+00 2.74e-01 3.79e+00 angle pdb=" N ALA A 468 " pdb=" CA ALA A 468 " pdb=" C ALA A 468 " ideal model delta sigma weight residual 111.02 113.92 -2.90 1.52e+00 4.33e-01 3.64e+00 ... (remaining 4980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.62: 1970 14.62 - 29.24: 99 29.24 - 43.87: 29 43.87 - 58.49: 8 58.49 - 73.11: 2 Dihedral angle restraints: 2108 sinusoidal: 785 harmonic: 1323 Sorted by residual: dihedral pdb=" CA THR A 308 " pdb=" C THR A 308 " pdb=" N GLU A 309 " pdb=" CA GLU A 309 " ideal model delta harmonic sigma weight residual -180.00 -163.82 -16.18 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ARG A 33 " pdb=" CB ARG A 33 " pdb=" CG ARG A 33 " pdb=" CD ARG A 33 " ideal model delta sinusoidal sigma weight residual -60.00 -115.47 55.47 3 1.50e+01 4.44e-03 9.35e+00 dihedral pdb=" CA ARG A 104 " pdb=" CB ARG A 104 " pdb=" CG ARG A 104 " pdb=" CD ARG A 104 " ideal model delta sinusoidal sigma weight residual 180.00 127.75 52.25 3 1.50e+01 4.44e-03 9.10e+00 ... (remaining 2105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 389 0.025 - 0.050: 100 0.050 - 0.075: 55 0.075 - 0.101: 24 0.101 - 0.126: 6 Chirality restraints: 574 Sorted by residual: chirality pdb=" CA THR A 176 " pdb=" N THR A 176 " pdb=" C THR A 176 " pdb=" CB THR A 176 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA ILE A 439 " pdb=" N ILE A 439 " pdb=" C ILE A 439 " pdb=" CB ILE A 439 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA ILE A 435 " pdb=" N ILE A 435 " pdb=" C ILE A 435 " pdb=" CB ILE A 435 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.12e-01 ... (remaining 571 not shown) Planarity restraints: 611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 238 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C VAL A 238 " 0.027 2.00e-02 2.50e+03 pdb=" O VAL A 238 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 239 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 239 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C VAL A 239 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL A 239 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 240 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 237 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C PHE A 237 " 0.026 2.00e-02 2.50e+03 pdb=" O PHE A 237 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 238 " -0.009 2.00e-02 2.50e+03 ... (remaining 608 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 887 2.80 - 3.32: 3828 3.32 - 3.85: 5935 3.85 - 4.37: 6627 4.37 - 4.90: 11289 Nonbonded interactions: 28566 Sorted by model distance: nonbonded pdb=" O LEU A 264 " pdb=" OG SER A 267 " model vdw 2.269 2.440 nonbonded pdb=" O ILE A 461 " pdb=" OG SER A 464 " model vdw 2.272 2.440 nonbonded pdb=" OG1 THR A 333 " pdb=" O GLY A 499 " model vdw 2.305 2.440 nonbonded pdb=" O LYS A 262 " pdb=" OG1 THR A 265 " model vdw 2.316 2.440 nonbonded pdb=" O CYS A 242 " pdb=" OG SER A 245 " model vdw 2.326 2.440 ... (remaining 28561 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 group one per residue 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.000 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.710 Find NCS groups from input model: 0.140 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:3.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.002 0.045 3672 Z= 0.125 Angle : 0.482 5.910 4985 Z= 0.259 Chirality : 0.034 0.126 574 Planarity : 0.004 0.029 611 Dihedral : 10.371 73.110 1262 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.75 % Allowed : 6.17 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.41), residues: 456 helix: 2.29 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -1.69 (0.60), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 332 HIS 0.001 0.000 HIS A 348 PHE 0.009 0.001 PHE A 198 TYR 0.006 0.001 TYR A 52 ARG 0.001 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 181 average time/residue: 0.1659 time to fit residues: 35.7221 Evaluate side-chains 99 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0412 time to fit residues: 0.7220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 41 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A 345 GLN ** A 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3672 Z= 0.196 Angle : 0.725 9.950 4985 Z= 0.343 Chirality : 0.040 0.153 574 Planarity : 0.005 0.060 611 Dihedral : 3.810 17.773 491 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.75 % Allowed : 18.50 % Favored : 77.75 % 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: 2.46 (0.40), residues: 456 helix: 2.43 (0.27), residues: 362 sheet: None (None), residues: 0 loop : -1.77 (0.59), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 69 HIS 0.002 0.001 HIS A 395 PHE 0.034 0.002 PHE A 417 TYR 0.015 0.002 TYR A 342 ARG 0.005 0.001 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.376 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 111 average time/residue: 0.1052 time to fit residues: 15.3795 Evaluate side-chains 102 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.436 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0413 time to fit residues: 1.0364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3672 Z= 0.184 Angle : 0.712 11.619 4985 Z= 0.334 Chirality : 0.039 0.148 574 Planarity : 0.005 0.048 611 Dihedral : 3.759 16.505 491 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.61 % Allowed : 21.98 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.40), residues: 456 helix: 2.22 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -1.91 (0.61), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 200 HIS 0.001 0.000 HIS A 521 PHE 0.046 0.002 PHE A 372 TYR 0.019 0.002 TYR A 477 ARG 0.003 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 0.401 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 105 average time/residue: 0.1166 time to fit residues: 15.9341 Evaluate side-chains 96 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.334 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0406 time to fit residues: 0.6418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 0.0050 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 337 GLN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3672 Z= 0.177 Angle : 0.710 11.267 4985 Z= 0.337 Chirality : 0.041 0.279 574 Planarity : 0.004 0.036 611 Dihedral : 3.810 16.142 491 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.49 % Allowed : 23.06 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.41), residues: 456 helix: 2.05 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -1.94 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 200 HIS 0.001 0.000 HIS A 303 PHE 0.057 0.002 PHE A 372 TYR 0.015 0.001 TYR A 477 ARG 0.009 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 113 average time/residue: 0.1129 time to fit residues: 16.6670 Evaluate side-chains 100 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1194 time to fit residues: 1.4094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.0470 chunk 18 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3672 Z= 0.178 Angle : 0.702 9.840 4985 Z= 0.333 Chirality : 0.040 0.150 574 Planarity : 0.004 0.040 611 Dihedral : 3.839 15.461 491 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.88 % Allowed : 27.61 % Favored : 70.51 % 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: 1.97 (0.41), residues: 456 helix: 2.05 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -1.93 (0.65), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 200 HIS 0.001 0.000 HIS A 303 PHE 0.057 0.002 PHE A 372 TYR 0.016 0.001 TYR A 444 ARG 0.006 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 103 average time/residue: 0.1101 time to fit residues: 15.0481 Evaluate side-chains 96 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.407 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0382 time to fit residues: 0.6137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3672 Z= 0.184 Angle : 0.761 11.981 4985 Z= 0.356 Chirality : 0.043 0.248 574 Planarity : 0.004 0.038 611 Dihedral : 3.936 17.378 491 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.22 % Allowed : 27.61 % Favored : 69.17 % 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: 1.92 (0.41), residues: 456 helix: 2.01 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -2.20 (0.66), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 200 HIS 0.000 0.000 HIS A 445 PHE 0.062 0.002 PHE A 372 TYR 0.013 0.001 TYR A 477 ARG 0.004 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.407 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 106 average time/residue: 0.1076 time to fit residues: 15.1534 Evaluate side-chains 96 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0388 time to fit residues: 0.9408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 0.0670 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3672 Z= 0.187 Angle : 0.830 14.944 4985 Z= 0.373 Chirality : 0.042 0.191 574 Planarity : 0.004 0.038 611 Dihedral : 4.036 17.623 491 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.34 % Allowed : 28.95 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.41), residues: 456 helix: 1.88 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -2.33 (0.66), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 200 HIS 0.000 0.000 HIS A 445 PHE 0.056 0.002 PHE A 372 TYR 0.013 0.001 TYR A 215 ARG 0.003 0.001 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.411 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 96 average time/residue: 0.1072 time to fit residues: 13.7179 Evaluate side-chains 94 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.399 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0371 time to fit residues: 0.6627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 0.0010 chunk 40 optimal weight: 10.0000 chunk 42 optimal weight: 0.0030 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 24 optimal weight: 0.2980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3672 Z= 0.189 Angle : 0.833 12.173 4985 Z= 0.375 Chirality : 0.044 0.267 574 Planarity : 0.004 0.035 611 Dihedral : 4.102 20.661 491 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.80 % Allowed : 28.95 % Favored : 70.24 % 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: 1.67 (0.41), residues: 456 helix: 1.86 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -2.40 (0.65), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 200 HIS 0.000 0.000 HIS A 348 PHE 0.049 0.001 PHE A 372 TYR 0.012 0.001 TYR A 477 ARG 0.004 0.001 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.381 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 95 average time/residue: 0.1081 time to fit residues: 13.7376 Evaluate side-chains 92 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0380 time to fit residues: 0.5958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.0870 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3672 Z= 0.196 Angle : 0.845 12.083 4985 Z= 0.382 Chirality : 0.044 0.252 574 Planarity : 0.004 0.037 611 Dihedral : 4.137 20.530 491 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.80 % Allowed : 29.22 % Favored : 69.97 % 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: 1.72 (0.41), residues: 456 helix: 1.91 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -2.46 (0.65), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 200 HIS 0.001 0.000 HIS A 521 PHE 0.052 0.002 PHE A 372 TYR 0.018 0.001 TYR A 215 ARG 0.004 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.403 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 94 average time/residue: 0.0963 time to fit residues: 12.2146 Evaluate side-chains 90 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.335 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0436 time to fit residues: 0.5882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 3672 Z= 0.211 Angle : 0.860 13.106 4985 Z= 0.390 Chirality : 0.043 0.188 574 Planarity : 0.004 0.035 611 Dihedral : 4.177 20.813 491 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.27 % Allowed : 29.49 % Favored : 70.24 % 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: 1.72 (0.41), residues: 456 helix: 1.92 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -2.52 (0.65), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 200 HIS 0.001 0.000 HIS A 445 PHE 0.050 0.002 PHE A 372 TYR 0.014 0.001 TYR A 477 ARG 0.003 0.000 ARG A 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.383 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.1038 time to fit residues: 13.0749 Evaluate side-chains 95 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.397 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.096809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.083476 restraints weight = 13613.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.085634 restraints weight = 7838.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.087117 restraints weight = 5227.979| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 3672 Z= 0.213 Angle : 0.864 12.459 4985 Z= 0.394 Chirality : 0.044 0.218 574 Planarity : 0.004 0.040 611 Dihedral : 4.272 21.071 491 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.27 % Allowed : 29.76 % Favored : 69.97 % 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: 1.69 (0.41), residues: 456 helix: 1.89 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -2.57 (0.65), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 200 HIS 0.002 0.000 HIS A 395 PHE 0.055 0.002 PHE A 372 TYR 0.019 0.001 TYR A 215 ARG 0.005 0.001 ARG A 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1132.77 seconds wall clock time: 21 minutes 24.66 seconds (1284.66 seconds total)