Starting phenix.real_space_refine on Thu Dec 7 18:37:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erc_28552/12_2023/8erc_28552.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erc_28552/12_2023/8erc_28552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erc_28552/12_2023/8erc_28552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erc_28552/12_2023/8erc_28552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erc_28552/12_2023/8erc_28552.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erc_28552/12_2023/8erc_28552.pdb" } resolution = 3.7 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= 0.715 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 24 5.16 5 C 2332 2.51 5 N 574 2.21 5 O 580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A ASP 145": "OD1" <-> "OD2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A ASP 220": "OD1" <-> "OD2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A ASP 308": "OD1" <-> "OD2" Residue "A TYR 331": "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: 3510 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3510 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 408} Time building chain proxies: 2.45, per 1000 atoms: 0.70 Number of scatterers: 3510 At special positions: 0 Unit cell: (80.025, 69.3, 80.025, 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 24 16.00 O 580 8.00 N 574 7.00 C 2332 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: 1.43 Conformation dependent library (CDL) restraints added in 753.8 milliseconds 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 822 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 1 sheets defined 80.0% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 2 through 24 removed outlier: 4.259A pdb=" N ILE A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) Proline residue: A 17 - end of helix removed outlier: 4.085A pdb=" N LYS A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 47 Processing helix chain 'A' and resid 49 through 67 removed outlier: 4.405A pdb=" N SER A 53 " --> pdb=" O HIS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 88 Processing helix chain 'A' and resid 88 through 93 Processing helix chain 'A' and resid 98 through 133 Processing helix chain 'A' and resid 148 through 157 Processing helix chain 'A' and resid 169 through 178 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 213 through 225 removed outlier: 3.709A pdb=" N ALA A 216 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 217 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASP A 220 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA A 221 " --> pdb=" O ARG A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 259 removed outlier: 4.307A pdb=" N ILE A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 3.731A pdb=" N ALA A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 303 through 309 Processing helix chain 'A' and resid 312 through 319 Processing helix chain 'A' and resid 321 through 332 Processing helix chain 'A' and resid 340 through 357 Processing helix chain 'A' and resid 359 through 384 removed outlier: 3.876A pdb=" N TYR A 363 " --> pdb=" O HIS A 359 " (cutoff:3.500A) Proline residue: A 370 - end of helix Processing helix chain 'A' and resid 388 through 417 removed outlier: 3.868A pdb=" N GLY A 413 " --> pdb=" O TYR A 409 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 429 Processing helix chain 'A' and resid 431 through 441 Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 265 248 hydrogen bonds defined for protein. 723 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: 0.83 Time building geometry restraints manager: 1.56 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: 1045 1.34 - 1.46: 877 1.46 - 1.58: 1676 1.58 - 1.70: 0 1.70 - 1.81: 36 Bond restraints: 3634 Sorted by residual: bond pdb=" CG PRO A 166 " pdb=" CD PRO A 166 " ideal model delta sigma weight residual 1.512 1.479 0.033 2.70e-02 1.37e+03 1.48e+00 bond pdb=" CA PRO A 166 " pdb=" C PRO A 166 " ideal model delta sigma weight residual 1.524 1.504 0.020 2.00e-02 2.50e+03 9.91e-01 bond pdb=" CB PRO A 166 " pdb=" CG PRO A 166 " ideal model delta sigma weight residual 1.506 1.469 0.037 3.90e-02 6.57e+02 9.16e-01 bond pdb=" C TRP A 196 " pdb=" N PRO A 197 " ideal model delta sigma weight residual 1.332 1.340 -0.008 8.90e-03 1.26e+04 7.96e-01 bond pdb=" CB HIS A 399 " pdb=" CG HIS A 399 " ideal model delta sigma weight residual 1.497 1.485 0.012 1.40e-02 5.10e+03 7.12e-01 ... (remaining 3629 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.66: 118 105.66 - 112.75: 1846 112.75 - 119.84: 1234 119.84 - 126.94: 1683 126.94 - 134.03: 83 Bond angle restraints: 4964 Sorted by residual: angle pdb=" C GLU A 129 " pdb=" N MET A 130 " pdb=" CA MET A 130 " ideal model delta sigma weight residual 121.58 115.03 6.55 1.95e+00 2.63e-01 1.13e+01 angle pdb=" CA GLU A 376 " pdb=" CB GLU A 376 " pdb=" CG GLU A 376 " ideal model delta sigma weight residual 114.10 108.79 5.31 2.00e+00 2.50e-01 7.06e+00 angle pdb=" N GLY A 357 " pdb=" CA GLY A 357 " pdb=" C GLY A 357 " ideal model delta sigma weight residual 110.63 114.43 -3.80 1.45e+00 4.76e-01 6.87e+00 angle pdb=" CA MET A 130 " pdb=" CB MET A 130 " pdb=" CG MET A 130 " ideal model delta sigma weight residual 114.10 119.08 -4.98 2.00e+00 2.50e-01 6.21e+00 angle pdb=" N MET A 130 " pdb=" CA MET A 130 " pdb=" CB MET A 130 " ideal model delta sigma weight residual 110.41 114.52 -4.11 1.68e+00 3.54e-01 5.97e+00 ... (remaining 4959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.59: 1873 15.59 - 31.18: 169 31.18 - 46.76: 45 46.76 - 62.35: 3 62.35 - 77.94: 3 Dihedral angle restraints: 2093 sinusoidal: 806 harmonic: 1287 Sorted by residual: dihedral pdb=" CG ARG A 378 " pdb=" CD ARG A 378 " pdb=" NE ARG A 378 " pdb=" CZ ARG A 378 " ideal model delta sinusoidal sigma weight residual 90.00 134.70 -44.70 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB LYS A 111 " pdb=" CG LYS A 111 " pdb=" CD LYS A 111 " pdb=" CE LYS A 111 " ideal model delta sinusoidal sigma weight residual -60.00 -110.97 50.97 3 1.50e+01 4.44e-03 8.96e+00 dihedral pdb=" CA GLU A 293 " pdb=" CB GLU A 293 " pdb=" CG GLU A 293 " pdb=" CD GLU A 293 " ideal model delta sinusoidal sigma weight residual 60.00 105.45 -45.45 3 1.50e+01 4.44e-03 8.17e+00 ... (remaining 2090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 312 0.026 - 0.052: 139 0.052 - 0.078: 49 0.078 - 0.105: 28 0.105 - 0.131: 9 Chirality restraints: 537 Sorted by residual: chirality pdb=" CA TRP A 196 " pdb=" N TRP A 196 " pdb=" C TRP A 196 " pdb=" CB TRP A 196 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA GLN A 65 " pdb=" N GLN A 65 " pdb=" C GLN A 65 " pdb=" CB GLN A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA PRO A 236 " pdb=" N PRO A 236 " pdb=" C PRO A 236 " pdb=" CB PRO A 236 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.43e-01 ... (remaining 534 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 426 " -0.011 2.00e-02 2.50e+03 9.86e-03 2.43e+00 pdb=" CG TRP A 426 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 426 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 426 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 426 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 426 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 426 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 426 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 426 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 426 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 165 " 0.024 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 166 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 166 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 166 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 377 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.96e+00 pdb=" C GLY A 377 " -0.024 2.00e-02 2.50e+03 pdb=" O GLY A 377 " 0.009 2.00e-02 2.50e+03 pdb=" N ARG A 378 " 0.008 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 29 2.67 - 3.23: 3563 3.23 - 3.79: 5816 3.79 - 4.34: 7102 4.34 - 4.90: 11674 Nonbonded interactions: 28184 Sorted by model distance: nonbonded pdb=" OH TYR A 246 " pdb=" OG1 THR A 307 " model vdw 2.115 2.440 nonbonded pdb=" OD1 ASN A 301 " pdb=" OG1 THR A 323 " model vdw 2.269 2.440 nonbonded pdb=" NH2 ARG A 405 " pdb=" OD2 ASP A 408 " model vdw 2.316 2.520 nonbonded pdb=" O TYR A 333 " pdb=" NH2 ARG A 344 " model vdw 2.330 2.520 nonbonded pdb=" O PHE A 205 " pdb=" OG SER A 209 " model vdw 2.334 2.440 ... (remaining 28179 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: 0.680 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: 3.090 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.390 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 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 : 0.003 0.037 3634 Z= 0.180 Angle : 0.671 7.145 4964 Z= 0.339 Chirality : 0.038 0.131 537 Planarity : 0.005 0.038 612 Dihedral : 12.915 77.940 1271 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.99 (0.41), residues: 439 helix: 1.62 (0.29), residues: 309 sheet: None (None), residues: 0 loop : 0.82 (0.61), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 426 HIS 0.005 0.001 HIS A 399 PHE 0.020 0.002 PHE A 245 TYR 0.015 0.001 TYR A 331 ARG 0.003 0.000 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.416 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1711 time to fit residues: 22.4806 Evaluate side-chains 95 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.453 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 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: 44 random chunks: chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3634 Z= 0.198 Angle : 0.634 7.454 4964 Z= 0.315 Chirality : 0.039 0.211 537 Planarity : 0.005 0.045 612 Dihedral : 3.452 11.700 490 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.93 % Allowed : 11.88 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.96 (0.41), residues: 439 helix: 1.64 (0.29), residues: 319 sheet: None (None), residues: 0 loop : 0.60 (0.63), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 426 HIS 0.004 0.001 HIS A 399 PHE 0.040 0.002 PHE A 22 TYR 0.021 0.002 TYR A 425 ARG 0.003 0.000 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.520 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 101 average time/residue: 0.1660 time to fit residues: 20.5384 Evaluate side-chains 100 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0369 time to fit residues: 0.6866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3634 Z= 0.197 Angle : 0.615 8.208 4964 Z= 0.301 Chirality : 0.038 0.132 537 Planarity : 0.004 0.040 612 Dihedral : 3.438 12.013 490 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.83 % Allowed : 16.85 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.96 (0.41), residues: 439 helix: 1.63 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.59 (0.64), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 196 HIS 0.003 0.001 HIS A 399 PHE 0.037 0.002 PHE A 232 TYR 0.021 0.002 TYR A 8 ARG 0.005 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 0.408 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 103 average time/residue: 0.1603 time to fit residues: 20.0623 Evaluate side-chains 100 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0366 time to fit residues: 0.6656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.0040 chunk 26 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 38 optimal weight: 0.0870 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 overall best weight: 0.5774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3634 Z= 0.174 Angle : 0.622 8.156 4964 Z= 0.301 Chirality : 0.039 0.239 537 Planarity : 0.004 0.041 612 Dihedral : 3.416 12.230 490 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.76 % Allowed : 18.23 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.10 (0.41), residues: 439 helix: 1.75 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.60 (0.65), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 196 HIS 0.002 0.001 HIS A 72 PHE 0.036 0.002 PHE A 232 TYR 0.025 0.002 TYR A 159 ARG 0.001 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 101 average time/residue: 0.1625 time to fit residues: 19.9798 Evaluate side-chains 98 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.402 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0515 time to fit residues: 0.8470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN A 123 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3634 Z= 0.336 Angle : 0.731 7.371 4964 Z= 0.373 Chirality : 0.043 0.291 537 Planarity : 0.005 0.044 612 Dihedral : 3.640 12.779 490 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.59 % Allowed : 18.51 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.46 (0.41), residues: 439 helix: 1.26 (0.28), residues: 328 sheet: None (None), residues: 0 loop : 0.35 (0.69), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 196 HIS 0.003 0.001 HIS A 49 PHE 0.040 0.002 PHE A 232 TYR 0.021 0.002 TYR A 159 ARG 0.003 0.001 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.418 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 103 average time/residue: 0.1669 time to fit residues: 20.8191 Evaluate side-chains 106 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0449 time to fit residues: 1.2626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 31 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3634 Z= 0.185 Angle : 0.648 7.871 4964 Z= 0.315 Chirality : 0.040 0.214 537 Planarity : 0.004 0.044 612 Dihedral : 3.477 12.922 490 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.38 % Allowed : 19.89 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.82 (0.42), residues: 439 helix: 1.56 (0.29), residues: 328 sheet: None (None), residues: 0 loop : 0.34 (0.69), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 6 HIS 0.002 0.001 HIS A 399 PHE 0.041 0.002 PHE A 232 TYR 0.012 0.001 TYR A 173 ARG 0.006 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 0.411 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 108 average time/residue: 0.1541 time to fit residues: 20.3471 Evaluate side-chains 100 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0625 time to fit residues: 0.5730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 26 optimal weight: 0.0980 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN A 123 HIS A 179 GLN A 399 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3634 Z= 0.182 Angle : 0.666 8.119 4964 Z= 0.320 Chirality : 0.041 0.308 537 Planarity : 0.005 0.043 612 Dihedral : 3.436 12.782 490 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.49 % Allowed : 21.27 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.95 (0.42), residues: 439 helix: 1.64 (0.29), residues: 327 sheet: None (None), residues: 0 loop : 0.45 (0.68), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 6 HIS 0.003 0.001 HIS A 72 PHE 0.040 0.002 PHE A 232 TYR 0.023 0.001 TYR A 159 ARG 0.006 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 103 average time/residue: 0.1582 time to fit residues: 19.9297 Evaluate side-chains 104 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.371 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0481 time to fit residues: 0.9684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3634 Z= 0.217 Angle : 0.708 9.075 4964 Z= 0.345 Chirality : 0.042 0.324 537 Planarity : 0.005 0.044 612 Dihedral : 3.480 12.973 490 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.83 % Allowed : 22.38 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.73 (0.41), residues: 439 helix: 1.49 (0.29), residues: 326 sheet: None (None), residues: 0 loop : 0.35 (0.68), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 426 HIS 0.003 0.001 HIS A 399 PHE 0.041 0.002 PHE A 232 TYR 0.027 0.002 TYR A 159 ARG 0.007 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 0.397 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 101 average time/residue: 0.1625 time to fit residues: 20.0256 Evaluate side-chains 95 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3634 Z= 0.192 Angle : 0.712 9.415 4964 Z= 0.341 Chirality : 0.043 0.335 537 Planarity : 0.005 0.044 612 Dihedral : 3.470 13.073 490 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.55 % Allowed : 23.76 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.93 (0.41), residues: 439 helix: 1.63 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.53 (0.65), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 6 HIS 0.003 0.001 HIS A 399 PHE 0.045 0.002 PHE A 232 TYR 0.024 0.002 TYR A 409 ARG 0.007 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 0.1606 time to fit residues: 19.5188 Evaluate side-chains 99 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0527 time to fit residues: 0.5625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 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 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3634 Z= 0.203 Angle : 0.743 11.285 4964 Z= 0.357 Chirality : 0.045 0.396 537 Planarity : 0.005 0.043 612 Dihedral : 3.496 13.149 490 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.10 % Allowed : 23.20 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.88 (0.41), residues: 439 helix: 1.61 (0.29), residues: 319 sheet: None (None), residues: 0 loop : 0.47 (0.65), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 327 HIS 0.003 0.001 HIS A 399 PHE 0.047 0.002 PHE A 232 TYR 0.024 0.002 TYR A 409 ARG 0.008 0.000 ARG A 242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 878 Ramachandran restraints generated. 439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.419 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 96 average time/residue: 0.1681 time to fit residues: 19.6358 Evaluate side-chains 97 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0447 time to fit residues: 0.7621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 0.0060 chunk 17 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 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 = 0.4331 r_free = 0.4331 target = 0.188708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.159884 restraints weight = 6182.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.165295 restraints weight = 3840.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.169179 restraints weight = 2684.786| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3634 Z= 0.197 Angle : 0.755 11.117 4964 Z= 0.362 Chirality : 0.046 0.381 537 Planarity : 0.005 0.044 612 Dihedral : 3.537 13.191 490 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.55 % Allowed : 23.48 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.87 (0.42), residues: 439 helix: 1.59 (0.29), residues: 319 sheet: None (None), residues: 0 loop : 0.49 (0.66), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 327 HIS 0.003 0.001 HIS A 399 PHE 0.046 0.002 PHE A 232 TYR 0.024 0.002 TYR A 159 ARG 0.008 0.000 ARG A 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1177.46 seconds wall clock time: 22 minutes 12.24 seconds (1332.24 seconds total)