Starting phenix.real_space_refine on Fri Dec 27 08:02:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8erc_28552/12_2024/8erc_28552.cif Found real_map, /net/cci-nas-00/data/ceres_data/8erc_28552/12_2024/8erc_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/cci-nas-00/data/ceres_data/8erc_28552/12_2024/8erc_28552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8erc_28552/12_2024/8erc_28552.map" model { file = "/net/cci-nas-00/data/ceres_data/8erc_28552/12_2024/8erc_28552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8erc_28552/12_2024/8erc_28552.cif" } 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. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 3.07, per 1000 atoms: 0.87 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 475.2 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: 0.44 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: 1.04 Time building geometry restraints manager: 1.09 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: 0.00 - 1.43: 4769 1.43 - 2.86: 138 2.86 - 4.29: 36 4.29 - 5.72: 15 5.72 - 7.15: 6 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 3.040 nonbonded pdb=" OD1 ASN A 301 " pdb=" OG1 THR A 323 " model vdw 2.269 3.040 nonbonded pdb=" NH2 ARG A 405 " pdb=" OD2 ASP A 408 " model vdw 2.316 3.120 nonbonded pdb=" O TYR A 333 " pdb=" NH2 ARG A 344 " model vdw 2.330 3.120 nonbonded pdb=" O PHE A 205 " pdb=" OG SER A 209 " model vdw 2.334 3.040 ... (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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.230 Find NCS groups from input model: 0.030 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:3.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.960 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6651 (tmm) cc_final: 0.6375 (tmm) REVERT: A 120 GLN cc_start: 0.6980 (tp40) cc_final: 0.6738 (tp-100) REVERT: A 146 VAL cc_start: 0.9489 (p) cc_final: 0.9284 (t) REVERT: A 160 VAL cc_start: 0.8703 (t) cc_final: 0.8377 (t) REVERT: A 231 LEU cc_start: 0.8757 (mt) cc_final: 0.8542 (tp) REVERT: A 254 CYS cc_start: 0.7844 (m) cc_final: 0.7420 (m) REVERT: A 412 MET cc_start: 0.7759 (mpp) cc_final: 0.6958 (mpp) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1691 time to fit residues: 22.2977 Evaluate side-chains 95 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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: 4.9990 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 0.0000 chunk 17 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.1475 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= 0.219 Angle : 0.648 7.911 4964 Z= 0.323 Chirality : 0.040 0.214 537 Planarity : 0.005 0.038 612 Dihedral : 3.453 11.598 490 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.21 % Allowed : 11.60 % 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: 1.98 (0.41), residues: 439 helix: 1.66 (0.28), residues: 319 sheet: None (None), residues: 0 loop : 0.57 (0.64), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 426 HIS 0.005 0.001 HIS A 399 PHE 0.037 0.002 PHE A 22 TYR 0.028 0.002 TYR A 425 ARG 0.003 0.000 ARG A 230 *********************** 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 109 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 146 VAL cc_start: 0.9503 (p) cc_final: 0.9282 (t) REVERT: A 254 CYS cc_start: 0.7904 (m) cc_final: 0.7511 (m) REVERT: A 409 TYR cc_start: 0.8725 (t80) cc_final: 0.8092 (t80) REVERT: A 412 MET cc_start: 0.7908 (mpp) cc_final: 0.7698 (mpp) outliers start: 8 outliers final: 3 residues processed: 102 average time/residue: 0.1649 time to fit residues: 20.4372 Evaluate side-chains 100 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 164 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 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 52 HIS A 120 GLN A 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3634 Z= 0.190 Angle : 0.616 8.348 4964 Z= 0.304 Chirality : 0.038 0.133 537 Planarity : 0.005 0.039 612 Dihedral : 3.523 11.520 490 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.93 % Allowed : 15.47 % Favored : 82.60 % 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: 2.00 (0.41), residues: 439 helix: 1.69 (0.28), residues: 321 sheet: None (None), residues: 0 loop : 0.51 (0.64), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 196 HIS 0.004 0.001 HIS A 399 PHE 0.037 0.002 PHE A 232 TYR 0.021 0.002 TYR A 159 ARG 0.007 0.001 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 to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7070 (mt) cc_final: 0.6867 (mm) REVERT: A 120 GLN cc_start: 0.7251 (tp40) cc_final: 0.6867 (tp-100) REVERT: A 146 VAL cc_start: 0.9501 (p) cc_final: 0.9291 (t) REVERT: A 150 MET cc_start: 0.6672 (tmm) cc_final: 0.6385 (tpt) REVERT: A 254 CYS cc_start: 0.7932 (m) cc_final: 0.7537 (m) outliers start: 7 outliers final: 5 residues processed: 100 average time/residue: 0.1552 time to fit residues: 19.4208 Evaluate side-chains 100 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 164 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 19 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS ** 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: 0.6600 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3634 Z= 0.169 Angle : 0.593 7.875 4964 Z= 0.290 Chirality : 0.038 0.211 537 Planarity : 0.005 0.041 612 Dihedral : 3.416 11.791 490 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.31 % Allowed : 17.13 % Favored : 79.56 % 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: 2.21 (0.41), residues: 439 helix: 1.85 (0.28), residues: 322 sheet: None (None), residues: 0 loop : 0.55 (0.64), residues: 117 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 0.020 0.002 TYR A 409 ARG 0.002 0.000 ARG A 230 *********************** 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 109 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLN cc_start: 0.7311 (tp40) cc_final: 0.6843 (tp-100) REVERT: A 130 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6534 (pmm) REVERT: A 150 MET cc_start: 0.6651 (tmm) cc_final: 0.6435 (tpt) REVERT: A 254 CYS cc_start: 0.7958 (m) cc_final: 0.7561 (m) outliers start: 12 outliers final: 7 residues processed: 101 average time/residue: 0.1484 time to fit residues: 18.5172 Evaluate side-chains 99 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 322 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.2393 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= 0.177 Angle : 0.613 8.249 4964 Z= 0.295 Chirality : 0.039 0.251 537 Planarity : 0.005 0.042 612 Dihedral : 3.410 11.831 490 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.59 % Allowed : 17.96 % Favored : 78.45 % 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: 2.34 (0.41), residues: 439 helix: 1.93 (0.28), residues: 322 sheet: None (None), residues: 0 loop : 0.62 (0.64), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 196 HIS 0.002 0.001 HIS A 72 PHE 0.036 0.002 PHE A 232 TYR 0.026 0.002 TYR A 159 ARG 0.002 0.000 ARG A 230 *********************** 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 110 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.7907 (tttt) cc_final: 0.7652 (tttt) REVERT: A 120 GLN cc_start: 0.7275 (tp40) cc_final: 0.6784 (tp-100) REVERT: A 130 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6415 (pmm) REVERT: A 150 MET cc_start: 0.6683 (tmm) cc_final: 0.6480 (tpt) REVERT: A 254 CYS cc_start: 0.7970 (m) cc_final: 0.7602 (m) outliers start: 13 outliers final: 8 residues processed: 102 average time/residue: 0.1544 time to fit residues: 19.3163 Evaluate side-chains 104 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 397 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 19 optimal weight: 0.0060 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3634 Z= 0.150 Angle : 0.604 8.523 4964 Z= 0.289 Chirality : 0.039 0.264 537 Planarity : 0.004 0.043 612 Dihedral : 3.357 11.809 490 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.31 % Allowed : 19.34 % Favored : 77.35 % 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: 2.40 (0.41), residues: 439 helix: 2.02 (0.29), residues: 322 sheet: None (None), residues: 0 loop : 0.53 (0.64), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 196 HIS 0.002 0.001 HIS A 72 PHE 0.040 0.002 PHE A 232 TYR 0.027 0.001 TYR A 409 ARG 0.002 0.000 ARG A 230 *********************** 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 113 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLN cc_start: 0.7276 (tp40) cc_final: 0.6780 (tp-100) REVERT: A 130 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6278 (pmm) REVERT: A 243 MET cc_start: 0.7542 (tpp) cc_final: 0.7206 (tpp) REVERT: A 254 CYS cc_start: 0.7956 (m) cc_final: 0.7547 (m) REVERT: A 376 GLU cc_start: 0.8180 (tp30) cc_final: 0.7710 (tp30) outliers start: 12 outliers final: 7 residues processed: 105 average time/residue: 0.1556 time to fit residues: 20.1832 Evaluate side-chains 105 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 397 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3634 Z= 0.160 Angle : 0.631 9.428 4964 Z= 0.295 Chirality : 0.040 0.319 537 Planarity : 0.005 0.043 612 Dihedral : 3.357 11.734 490 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.76 % Allowed : 19.34 % 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: 2.39 (0.41), residues: 439 helix: 2.00 (0.29), residues: 322 sheet: None (None), residues: 0 loop : 0.57 (0.64), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 196 HIS 0.004 0.001 HIS A 123 PHE 0.040 0.002 PHE A 232 TYR 0.028 0.002 TYR A 159 ARG 0.003 0.000 ARG A 127 *********************** 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 to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.7767 (tttt) cc_final: 0.7525 (tttt) REVERT: A 120 GLN cc_start: 0.7172 (tp40) cc_final: 0.6733 (tp-100) REVERT: A 130 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.6318 (pmm) REVERT: A 234 MET cc_start: 0.5530 (ppp) cc_final: 0.5280 (ppp) REVERT: A 243 MET cc_start: 0.7520 (tpp) cc_final: 0.7297 (tpp) REVERT: A 254 CYS cc_start: 0.7811 (m) cc_final: 0.7437 (m) REVERT: A 376 GLU cc_start: 0.8188 (tp30) cc_final: 0.7710 (tp30) outliers start: 10 outliers final: 8 residues processed: 103 average time/residue: 0.1511 time to fit residues: 19.3101 Evaluate side-chains 108 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 397 TRP Chi-restraints excluded: chain A residue 411 CYS 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: 0.9990 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 123 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.2842 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= 0.194 Angle : 0.657 9.273 4964 Z= 0.312 Chirality : 0.041 0.373 537 Planarity : 0.005 0.044 612 Dihedral : 3.358 12.046 490 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.31 % Allowed : 19.89 % 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: 2.37 (0.41), residues: 439 helix: 1.98 (0.29), residues: 322 sheet: None (None), residues: 0 loop : 0.54 (0.65), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 196 HIS 0.003 0.001 HIS A 72 PHE 0.041 0.002 PHE A 232 TYR 0.026 0.002 TYR A 409 ARG 0.003 0.000 ARG A 230 *********************** 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 106 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.7893 (tttt) cc_final: 0.7599 (tttt) REVERT: A 120 GLN cc_start: 0.7232 (tp40) cc_final: 0.6742 (tp-100) REVERT: A 130 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.6272 (pmm) REVERT: A 234 MET cc_start: 0.5607 (ppp) cc_final: 0.5399 (ppp) REVERT: A 243 MET cc_start: 0.7537 (tpp) cc_final: 0.7303 (tpp) REVERT: A 376 GLU cc_start: 0.8309 (tp30) cc_final: 0.7833 (tp30) REVERT: A 409 TYR cc_start: 0.8784 (t80) cc_final: 0.8462 (t80) outliers start: 12 outliers final: 9 residues processed: 99 average time/residue: 0.1502 time to fit residues: 18.3105 Evaluate side-chains 107 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 397 TRP Chi-restraints excluded: chain A residue 411 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 19 optimal weight: 0.0060 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3634 Z= 0.253 Angle : 0.691 9.395 4964 Z= 0.337 Chirality : 0.043 0.383 537 Planarity : 0.005 0.044 612 Dihedral : 3.432 12.216 490 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.87 % Allowed : 20.44 % 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: 2.17 (0.41), residues: 439 helix: 1.85 (0.28), residues: 322 sheet: None (None), residues: 0 loop : 0.42 (0.64), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 196 HIS 0.004 0.001 HIS A 123 PHE 0.044 0.002 PHE A 232 TYR 0.031 0.002 TYR A 409 ARG 0.008 0.001 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 108 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8003 (tttt) cc_final: 0.7753 (tttt) REVERT: A 120 GLN cc_start: 0.7136 (tp40) cc_final: 0.6713 (tp-100) REVERT: A 130 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6377 (pmm) REVERT: A 234 MET cc_start: 0.5642 (ppp) cc_final: 0.5426 (ppp) REVERT: A 243 MET cc_start: 0.7503 (tpp) cc_final: 0.7184 (tpp) REVERT: A 376 GLU cc_start: 0.8310 (tp30) cc_final: 0.7809 (tp30) outliers start: 14 outliers final: 11 residues processed: 100 average time/residue: 0.1547 time to fit residues: 19.0765 Evaluate side-chains 101 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 397 TRP Chi-restraints excluded: chain A residue 411 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.3030 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 : 0.693 10.549 4964 Z= 0.324 Chirality : 0.043 0.382 537 Planarity : 0.005 0.044 612 Dihedral : 3.428 12.588 490 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.76 % Allowed : 22.10 % Favored : 75.14 % 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: 2.20 (0.41), residues: 439 helix: 1.91 (0.29), residues: 325 sheet: None (None), residues: 0 loop : 0.28 (0.64), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 196 HIS 0.003 0.001 HIS A 72 PHE 0.045 0.002 PHE A 232 TYR 0.034 0.002 TYR A 409 ARG 0.003 0.000 ARG A 230 ********************** 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 101 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.7906 (tttt) cc_final: 0.7605 (tttt) REVERT: A 120 GLN cc_start: 0.7182 (tp40) cc_final: 0.6729 (tp-100) REVERT: A 130 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6314 (pmm) REVERT: A 234 MET cc_start: 0.5651 (ppp) cc_final: 0.5450 (ppp) REVERT: A 243 MET cc_start: 0.7529 (tpp) cc_final: 0.7229 (tpp) REVERT: A 376 GLU cc_start: 0.8294 (tp30) cc_final: 0.7845 (tp30) outliers start: 10 outliers final: 8 residues processed: 96 average time/residue: 0.1458 time to fit residues: 17.4459 Evaluate side-chains 98 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 397 TRP Chi-restraints excluded: chain A residue 411 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.186657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.158179 restraints weight = 6327.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.163360 restraints weight = 3989.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.167331 restraints weight = 2793.528| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3634 Z= 0.179 Angle : 0.691 10.720 4964 Z= 0.322 Chirality : 0.043 0.381 537 Planarity : 0.005 0.044 612 Dihedral : 3.449 15.222 490 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.76 % Allowed : 22.93 % Favored : 74.31 % 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: 2.20 (0.41), residues: 439 helix: 1.90 (0.29), residues: 325 sheet: None (None), residues: 0 loop : 0.31 (0.65), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 249 HIS 0.003 0.001 HIS A 72 PHE 0.044 0.002 PHE A 232 TYR 0.031 0.002 TYR A 409 ARG 0.003 0.000 ARG A 230 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1211.34 seconds wall clock time: 22 minutes 58.54 seconds (1378.54 seconds total)