Starting phenix.real_space_refine on Fri Apr 5 15:48:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erc_28552/04_2024/8erc_28552.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erc_28552/04_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erc_28552/04_2024/8erc_28552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erc_28552/04_2024/8erc_28552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erc_28552/04_2024/8erc_28552.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erc_28552/04_2024/8erc_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-dev-5288/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: 2.49, per 1000 atoms: 0.71 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: 1.50 Conformation dependent library (CDL) restraints added in 824.1 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: 0.38 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: 0.97 Time building geometry restraints manager: 1.64 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: 0.010 Normalize map: mean=0, sd=1: 1.980 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: 3.180 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 15.350 Find NCS groups from input model: 0.090 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.430 ------------------------------------------------------------------------------- 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 : 0.350 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: 0.1644 time to fit residues: 21.5578 Evaluate side-chains 95 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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: 0.6980 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 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: 0.6609 moved from start: 0.1425 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= 0.194 Angle : 0.632 8.130 4964 Z= 0.312 Chirality : 0.039 0.209 537 Planarity : 0.005 0.045 612 Dihedral : 3.438 11.748 490 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.21 % Allowed : 11.33 % Favored : 86.46 % 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: 2.03 (0.41), residues: 439 helix: 1.69 (0.29), residues: 319 sheet: None (None), residues: 0 loop : 0.59 (0.64), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 426 HIS 0.005 0.001 HIS A 399 PHE 0.037 0.002 PHE A 22 TYR 0.030 0.002 TYR A 425 ARG 0.003 0.000 ARG A 405 *********************** 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 108 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 52 HIS cc_start: 0.6539 (m90) cc_final: 0.6205 (m90) REVERT: A 146 VAL cc_start: 0.9504 (p) cc_final: 0.9282 (t) REVERT: A 254 CYS cc_start: 0.7830 (m) cc_final: 0.7430 (m) REVERT: A 409 TYR cc_start: 0.8698 (t80) cc_final: 0.7944 (t80) REVERT: A 412 MET cc_start: 0.7923 (mpp) cc_final: 0.7710 (mpp) outliers start: 8 outliers final: 4 residues processed: 101 average time/residue: 0.1637 time to fit residues: 20.1221 Evaluate side-chains 103 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 158 CYS 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: 0.2980 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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: 0.6588 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3634 Z= 0.177 Angle : 0.603 8.209 4964 Z= 0.295 Chirality : 0.037 0.134 537 Planarity : 0.004 0.040 612 Dihedral : 3.448 11.771 490 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.49 % Allowed : 14.64 % Favored : 82.87 % 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: 2.05 (0.41), residues: 439 helix: 1.72 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.56 (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 0.035 0.002 PHE A 232 TYR 0.019 0.002 TYR A 159 ARG 0.004 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 111 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 HIS cc_start: 0.6610 (m90) cc_final: 0.6287 (m90) REVERT: A 120 GLN cc_start: 0.7247 (tp40) cc_final: 0.6861 (tp-100) REVERT: A 146 VAL cc_start: 0.9494 (p) cc_final: 0.9274 (t) REVERT: A 150 MET cc_start: 0.6662 (tmm) cc_final: 0.6367 (tpt) REVERT: A 234 MET cc_start: 0.6192 (ppp) cc_final: 0.5964 (ppp) REVERT: A 254 CYS cc_start: 0.7864 (m) cc_final: 0.7453 (m) REVERT: A 409 TYR cc_start: 0.8711 (t80) cc_final: 0.8030 (t80) outliers start: 9 outliers final: 7 residues processed: 103 average time/residue: 0.1525 time to fit residues: 19.1190 Evaluate side-chains 105 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 158 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 404 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.0170 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 1.1220 ------------------------------------------------------------------------------- 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: 0.6643 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3634 Z= 0.211 Angle : 0.611 7.914 4964 Z= 0.299 Chirality : 0.039 0.261 537 Planarity : 0.004 0.041 612 Dihedral : 3.392 12.141 490 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.14 % Allowed : 16.57 % Favored : 79.28 % 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: 1.68 (0.28), residues: 328 sheet: None (None), residues: 0 loop : 0.40 (0.68), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 196 HIS 0.002 0.000 HIS A 72 PHE 0.038 0.002 PHE A 232 TYR 0.024 0.002 TYR A 159 ARG 0.001 0.000 ARG A 405 *********************** 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 116 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 HIS cc_start: 0.6729 (m90) cc_final: 0.6446 (m90) REVERT: A 120 GLN cc_start: 0.7184 (tp40) cc_final: 0.6767 (tp-100) REVERT: A 130 MET cc_start: 0.7183 (OUTLIER) cc_final: 0.6547 (pmm) REVERT: A 146 VAL cc_start: 0.9504 (p) cc_final: 0.9289 (t) REVERT: A 150 MET cc_start: 0.6648 (tmm) cc_final: 0.6363 (tpt) REVERT: A 243 MET cc_start: 0.7612 (tpp) cc_final: 0.7309 (tpp) REVERT: A 254 CYS cc_start: 0.7746 (m) cc_final: 0.7343 (m) REVERT: A 376 GLU cc_start: 0.7926 (tp30) cc_final: 0.7616 (tp30) outliers start: 15 outliers final: 9 residues processed: 106 average time/residue: 0.1570 time to fit residues: 20.2825 Evaluate side-chains 107 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 158 CYS 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=3.50 ------------------------------------------------------------------------------- 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: 6.9990 chunk 17 optimal weight: 0.1980 chunk 36 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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: 0.6648 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3634 Z= 0.199 Angle : 0.625 7.924 4964 Z= 0.304 Chirality : 0.039 0.254 537 Planarity : 0.004 0.043 612 Dihedral : 3.395 12.558 490 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.87 % Allowed : 17.96 % Favored : 78.18 % 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: 1.68 (0.28), residues: 328 sheet: None (None), residues: 0 loop : 0.44 (0.69), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 196 HIS 0.003 0.001 HIS A 72 PHE 0.039 0.002 PHE A 232 TYR 0.025 0.002 TYR A 409 ARG 0.002 0.000 ARG A 300 *********************** 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 114 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 HIS cc_start: 0.6691 (m90) cc_final: 0.6313 (m90) REVERT: A 120 GLN cc_start: 0.7093 (tp40) cc_final: 0.6712 (tp-100) REVERT: A 130 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6527 (pmm) REVERT: A 146 VAL cc_start: 0.9498 (p) cc_final: 0.9289 (t) REVERT: A 150 MET cc_start: 0.6593 (tmm) cc_final: 0.6379 (tpt) REVERT: A 243 MET cc_start: 0.7628 (tpp) cc_final: 0.7394 (tpp) REVERT: A 254 CYS cc_start: 0.7880 (m) cc_final: 0.7503 (m) REVERT: A 376 GLU cc_start: 0.8046 (tp30) cc_final: 0.7645 (tp30) outliers start: 14 outliers final: 9 residues processed: 105 average time/residue: 0.1532 time to fit residues: 19.5439 Evaluate side-chains 108 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 158 CYS 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: 0.5980 chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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: 0.6607 moved from start: 0.2490 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= 0.179 Angle : 0.628 8.610 4964 Z= 0.300 Chirality : 0.039 0.289 537 Planarity : 0.004 0.043 612 Dihedral : 3.366 12.343 490 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.59 % Allowed : 19.06 % 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: 2.29 (0.41), residues: 439 helix: 1.88 (0.28), residues: 322 sheet: None (None), residues: 0 loop : 0.67 (0.66), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 196 HIS 0.003 0.001 HIS A 72 PHE 0.042 0.002 PHE A 232 TYR 0.028 0.002 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 115 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 HIS cc_start: 0.6596 (m90) cc_final: 0.6266 (m90) REVERT: A 120 GLN cc_start: 0.7073 (tp40) cc_final: 0.6760 (tp40) REVERT: A 130 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6484 (pmm) REVERT: A 146 VAL cc_start: 0.9499 (p) cc_final: 0.9293 (t) REVERT: A 234 MET cc_start: 0.5601 (ppp) cc_final: 0.5395 (ppp) REVERT: A 243 MET cc_start: 0.7589 (tpp) cc_final: 0.7304 (tpp) REVERT: A 254 CYS cc_start: 0.7866 (m) cc_final: 0.7454 (m) REVERT: A 376 GLU cc_start: 0.8136 (tp30) cc_final: 0.7733 (tp30) outliers start: 13 outliers final: 9 residues processed: 106 average time/residue: 0.1559 time to fit residues: 20.1387 Evaluate side-chains 109 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 158 CYS 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: 0.5980 chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.0010 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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: 0.6574 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3634 Z= 0.167 Angle : 0.628 8.669 4964 Z= 0.298 Chirality : 0.040 0.344 537 Planarity : 0.005 0.043 612 Dihedral : 3.367 12.253 490 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.59 % Allowed : 19.06 % 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: 2.31 (0.41), residues: 439 helix: 1.90 (0.29), residues: 322 sheet: None (None), residues: 0 loop : 0.64 (0.66), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 196 HIS 0.007 0.001 HIS A 123 PHE 0.041 0.002 PHE A 232 TYR 0.027 0.002 TYR A 159 ARG 0.004 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 115 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 HIS cc_start: 0.6541 (m90) cc_final: 0.6188 (m90) REVERT: A 130 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6419 (pmm) REVERT: A 243 MET cc_start: 0.7545 (tpp) cc_final: 0.7218 (tpp) REVERT: A 254 CYS cc_start: 0.7721 (m) cc_final: 0.7304 (m) REVERT: A 308 ASP cc_start: 0.7941 (t0) cc_final: 0.7501 (t0) REVERT: A 376 GLU cc_start: 0.8116 (tp30) cc_final: 0.7709 (tp30) outliers start: 13 outliers final: 8 residues processed: 108 average time/residue: 0.1518 time to fit residues: 20.1077 Evaluate side-chains 108 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 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: 0.6651 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3634 Z= 0.234 Angle : 0.697 9.193 4964 Z= 0.339 Chirality : 0.042 0.381 537 Planarity : 0.005 0.044 612 Dihedral : 3.472 12.509 490 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.59 % Allowed : 18.78 % Favored : 77.62 % 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: 1.82 (0.28), residues: 321 sheet: None (None), residues: 0 loop : 0.64 (0.66), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 249 HIS 0.002 0.001 HIS A 72 PHE 0.046 0.002 PHE A 232 TYR 0.030 0.002 TYR A 409 ARG 0.002 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 111 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 HIS cc_start: 0.6668 (m90) cc_final: 0.6256 (m90) REVERT: A 120 GLN cc_start: 0.7175 (tp40) cc_final: 0.6854 (tp-100) REVERT: A 130 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6366 (pmm) REVERT: A 242 ARG cc_start: 0.8151 (ttp-110) cc_final: 0.7801 (ttp-110) REVERT: A 243 MET cc_start: 0.7594 (tpp) cc_final: 0.7206 (tpp) REVERT: A 376 GLU cc_start: 0.8146 (tp30) cc_final: 0.7709 (tp30) outliers start: 13 outliers final: 10 residues processed: 104 average time/residue: 0.1623 time to fit residues: 20.5556 Evaluate side-chains 106 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 151 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 19 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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: 0.6648 moved from start: 0.2886 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= 0.221 Angle : 0.697 10.233 4964 Z= 0.337 Chirality : 0.043 0.371 537 Planarity : 0.005 0.044 612 Dihedral : 3.506 12.460 490 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.59 % Allowed : 19.89 % Favored : 76.52 % 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: 2.09 (0.41), residues: 439 helix: 1.74 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.59 (0.66), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 176 HIS 0.003 0.001 HIS A 123 PHE 0.038 0.002 PHE A 232 TYR 0.033 0.002 TYR A 409 ARG 0.003 0.000 ARG A 127 *********************** 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 105 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6389 (pmm) REVERT: A 243 MET cc_start: 0.7595 (tpp) cc_final: 0.7195 (tpp) REVERT: A 376 GLU cc_start: 0.8154 (tp30) cc_final: 0.7718 (tp30) outliers start: 13 outliers final: 12 residues processed: 98 average time/residue: 0.1639 time to fit residues: 19.6268 Evaluate side-chains 104 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 71 CYS 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 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.9358 > 50: distance: 2 - 19: 20.388 distance: 6 - 29: 35.595 distance: 12 - 37: 13.554 distance: 15 - 19: 21.711 distance: 19 - 20: 16.125 distance: 20 - 21: 22.919 distance: 20 - 23: 18.797 distance: 21 - 22: 13.581 distance: 21 - 29: 33.106 distance: 23 - 24: 6.793 distance: 24 - 25: 12.934 distance: 24 - 26: 14.178 distance: 25 - 27: 14.151 distance: 26 - 28: 13.612 distance: 27 - 28: 28.470 distance: 29 - 30: 11.081 distance: 30 - 31: 28.688 distance: 30 - 33: 13.217 distance: 31 - 32: 29.929 distance: 31 - 37: 12.327 distance: 34 - 35: 41.574 distance: 34 - 36: 51.404 distance: 37 - 38: 4.490 distance: 38 - 39: 14.851 distance: 38 - 41: 16.132 distance: 39 - 40: 18.569 distance: 39 - 48: 46.963 distance: 41 - 42: 18.100 distance: 42 - 43: 3.816 distance: 42 - 44: 18.030 distance: 43 - 45: 20.234 distance: 44 - 46: 11.999 distance: 45 - 47: 14.362 distance: 46 - 47: 16.951 distance: 48 - 49: 9.456 distance: 48 - 54: 20.882 distance: 49 - 50: 16.481 distance: 49 - 52: 5.046 distance: 50 - 51: 4.918 distance: 50 - 55: 37.985 distance: 52 - 53: 21.098 distance: 53 - 54: 6.365 distance: 55 - 56: 6.008 distance: 56 - 57: 3.438 distance: 56 - 59: 3.972 distance: 57 - 58: 16.250 distance: 57 - 63: 14.593 distance: 59 - 60: 9.287 distance: 60 - 61: 20.059 distance: 60 - 62: 6.782 distance: 63 - 64: 3.015 distance: 64 - 65: 9.502 distance: 64 - 67: 6.008 distance: 65 - 72: 30.372 distance: 66 - 84: 22.608 distance: 67 - 68: 9.782 distance: 68 - 69: 18.377 distance: 69 - 70: 12.534 distance: 69 - 71: 14.568 distance: 72 - 73: 27.295 distance: 73 - 74: 11.241 distance: 73 - 76: 19.590 distance: 74 - 75: 29.523 distance: 74 - 77: 8.552 distance: 75 - 95: 21.426 distance: 77 - 78: 12.543 distance: 78 - 79: 18.262 distance: 78 - 81: 16.369 distance: 79 - 80: 27.190 distance: 79 - 84: 23.738 distance: 81 - 82: 12.987 distance: 81 - 83: 6.838 distance: 84 - 85: 15.616 distance: 85 - 86: 7.276 distance: 85 - 88: 14.230 distance: 86 - 87: 15.733 distance: 86 - 95: 19.708 distance: 88 - 89: 5.295 distance: 89 - 90: 7.915 distance: 90 - 91: 11.928 distance: 91 - 92: 3.796 distance: 95 - 96: 6.005 distance: 96 - 97: 8.978 distance: 96 - 99: 12.720 distance: 97 - 98: 4.311 distance: 97 - 104: 22.455 distance: 98 - 115: 21.504 distance: 99 - 100: 9.283 distance: 100 - 101: 7.766 distance: 101 - 102: 9.115 distance: 101 - 103: 14.667