Starting phenix.real_space_refine on Wed Jan 17 16:28:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkw_14055/01_2024/7qkw_14055.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkw_14055/01_2024/7qkw_14055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkw_14055/01_2024/7qkw_14055.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkw_14055/01_2024/7qkw_14055.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkw_14055/01_2024/7qkw_14055.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkw_14055/01_2024/7qkw_14055.pdb" } resolution = 2.32 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= 0.002 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: 5 Type Number sf(0) Gaussians S 12 5.16 5 C 1419 2.51 5 N 405 2.21 5 O 432 1.98 5 H 2439 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 4707 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 823 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "A" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 823 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 823 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 746 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "E" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 746 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "F" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 746 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Time building chain proxies: 2.46, per 1000 atoms: 0.52 Number of scatterers: 4707 At special positions: 0 Unit cell: (84.872, 84.048, 31.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 O 432 8.00 N 405 7.00 C 1419 6.00 H 2439 1.00 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: 3.64 Conformation dependent library (CDL) restraints added in 470.9 milliseconds 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 552 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 43.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 276 through 283 removed outlier: 6.502A pdb=" N GLN B 276 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ASN C 279 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE B 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N LYS C 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS B 280 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ASP C 283 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU B 282 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 291 removed outlier: 6.895A pdb=" N SER B 289 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS A 290 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N CYS B 291 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL B 287 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LYS C 290 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER B 289 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 297 through 298 removed outlier: 6.428A pdb=" N ILE B 297 " --> pdb=" O LYS C 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.240A pdb=" N VAL B 306 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL A 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE B 308 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 314 removed outlier: 7.191A pdb=" N VAL B 313 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 322 removed outlier: 6.452A pdb=" N LYS B 317 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N SER A 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR B 319 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N CYS A 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS B 321 " --> pdb=" O CYS A 322 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 276 through 283 removed outlier: 6.437A pdb=" N ILE D 277 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LYS E 280 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN D 279 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LEU E 282 " --> pdb=" O ASN D 279 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS D 281 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLN D 276 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASN F 279 " --> pdb=" O GLN D 276 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE D 278 " --> pdb=" O ASN F 279 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LYS F 281 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS D 280 " --> pdb=" O LYS F 281 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASP F 283 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU D 282 " --> pdb=" O ASP F 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 286 through 291 removed outlier: 6.955A pdb=" N VAL E 287 " --> pdb=" O ASN D 286 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLN D 288 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL D 287 " --> pdb=" O GLN F 288 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LYS F 290 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER D 289 " --> pdb=" O LYS F 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 297 through 298 removed outlier: 6.545A pdb=" N ILE D 297 " --> pdb=" O LYS F 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 306 through 310 Processing sheet with id=AB2, first strand: chain 'E' and resid 313 through 314 removed outlier: 7.114A pdb=" N VAL D 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 317 through 321 removed outlier: 6.559A pdb=" N VAL D 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) 37 hydrogen bonds defined for protein. 111 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: 1.48 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 2427 1.12 - 1.30: 381 1.30 - 1.47: 731 1.47 - 1.64: 1174 1.64 - 1.82: 12 Bond restraints: 4725 Sorted by residual: bond pdb=" N VAL A 275 " pdb=" H VAL A 275 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE2 GLN A 276 " pdb="HE21 GLN A 276 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LYS A 317 " pdb=" H LYS A 317 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ASP E 295 " pdb=" H ASP E 295 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" NE2 GLN C 276 " pdb="HE22 GLN C 276 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 4720 not shown) Histogram of bond angle deviations from ideal: 96.69 - 103.23: 28 103.23 - 109.78: 4039 109.78 - 116.33: 2377 116.33 - 122.88: 1868 122.88 - 129.43: 337 Bond angle restraints: 8649 Sorted by residual: angle pdb=" C VAL F 300 " pdb=" N PRO F 301 " pdb=" CA PRO F 301 " ideal model delta sigma weight residual 119.24 125.09 -5.85 1.04e+00 9.25e-01 3.16e+01 angle pdb=" C VAL D 300 " pdb=" N PRO D 301 " pdb=" CA PRO D 301 " ideal model delta sigma weight residual 119.24 125.00 -5.76 1.04e+00 9.25e-01 3.06e+01 angle pdb=" CB HIS D 299 " pdb=" CG HIS D 299 " pdb=" CD2 HIS D 299 " ideal model delta sigma weight residual 131.20 125.22 5.98 1.30e+00 5.92e-01 2.12e+01 angle pdb=" C ASP F 314 " pdb=" N LEU F 315 " pdb=" CA LEU F 315 " ideal model delta sigma weight residual 122.37 129.43 -7.06 1.54e+00 4.22e-01 2.10e+01 angle pdb=" CA LYS E 311 " pdb=" C LYS E 311 " pdb=" N PRO E 312 " ideal model delta sigma weight residual 118.16 121.36 -3.20 7.00e-01 2.04e+00 2.09e+01 ... (remaining 8644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.91: 1851 14.91 - 29.83: 156 29.83 - 44.74: 28 44.74 - 59.65: 37 59.65 - 74.56: 43 Dihedral angle restraints: 2115 sinusoidal: 1215 harmonic: 900 Sorted by residual: dihedral pdb=" CA ILE E 297 " pdb=" C ILE E 297 " pdb=" N LYS E 298 " pdb=" CA LYS E 298 " ideal model delta harmonic sigma weight residual 180.00 -151.92 -28.08 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA ILE D 297 " pdb=" C ILE D 297 " pdb=" N LYS D 298 " pdb=" CA LYS D 298 " ideal model delta harmonic sigma weight residual 180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA SER C 285 " pdb=" C SER C 285 " pdb=" N ASN C 286 " pdb=" CA ASN C 286 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 2112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 216 0.071 - 0.142: 99 0.142 - 0.214: 43 0.214 - 0.285: 11 0.285 - 0.356: 3 Chirality restraints: 372 Sorted by residual: chirality pdb=" CA GLN A 288 " pdb=" N GLN A 288 " pdb=" C GLN A 288 " pdb=" CB GLN A 288 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA PRO F 301 " pdb=" N PRO F 301 " pdb=" C PRO F 301 " pdb=" CB PRO F 301 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA ASN B 296 " pdb=" N ASN B 296 " pdb=" C ASN B 296 " pdb=" CB ASN B 296 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 369 not shown) Planarity restraints: 669 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 299 " -0.099 2.00e-02 2.50e+03 5.35e-02 6.44e+01 pdb=" CG HIS A 299 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS A 299 " 0.054 2.00e-02 2.50e+03 pdb=" CD2 HIS A 299 " 0.044 2.00e-02 2.50e+03 pdb=" CE1 HIS A 299 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS A 299 " -0.025 2.00e-02 2.50e+03 pdb=" HD2 HIS A 299 " 0.057 2.00e-02 2.50e+03 pdb=" HE1 HIS A 299 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 HIS A 299 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 288 " 0.062 2.00e-02 2.50e+03 5.92e-02 5.25e+01 pdb=" CD GLN C 288 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLN C 288 " -0.057 2.00e-02 2.50e+03 pdb=" NE2 GLN C 288 " 0.016 2.00e-02 2.50e+03 pdb="HE21 GLN C 288 " -0.082 2.00e-02 2.50e+03 pdb="HE22 GLN C 288 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 288 " 0.062 2.00e-02 2.50e+03 5.72e-02 4.91e+01 pdb=" CD GLN B 288 " -0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN B 288 " -0.054 2.00e-02 2.50e+03 pdb=" NE2 GLN B 288 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN B 288 " -0.075 2.00e-02 2.50e+03 pdb="HE22 GLN B 288 " 0.084 2.00e-02 2.50e+03 ... (remaining 666 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 396 2.18 - 2.79: 8449 2.79 - 3.39: 12554 3.39 - 4.00: 17045 4.00 - 4.60: 23633 Nonbonded interactions: 62077 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.576 1.850 nonbonded pdb=" OD1 ASP F 283 " pdb=" HG SER F 285 " model vdw 1.589 1.850 nonbonded pdb=" OD1 ASP E 283 " pdb=" HG SER E 285 " model vdw 1.600 1.850 nonbonded pdb=" OD1 ASP D 283 " pdb=" HG SER D 285 " model vdw 1.612 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.612 1.850 ... (remaining 62072 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 275 through 322) selection = (chain 'B' and resid 275 through 322) selection = (chain 'C' and resid 275 through 322) selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 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: 0.070 Extract box with map and model: 11.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.220 Find NCS groups from input model: 0.240 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:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.010 0.032 2286 Z= 0.694 Angle : 1.934 7.092 3063 Z= 1.278 Chirality : 0.098 0.356 372 Planarity : 0.010 0.059 381 Dihedral : 13.527 74.563 885 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.37), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.29), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.024 0.009 HIS A 299 TYR 0.050 0.015 TYR D 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 ASP cc_start: 0.7772 (t0) cc_final: 0.7438 (t70) REVERT: A 317 LYS cc_start: 0.7443 (tptm) cc_final: 0.6787 (pmtt) REVERT: E 321 LYS cc_start: 0.7596 (mtmm) cc_final: 0.7197 (pmtt) REVERT: F 321 LYS cc_start: 0.7052 (mtmt) cc_final: 0.6581 (mmtt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 2.2897 time to fit residues: 184.7789 Evaluate side-chains 35 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN A 286 ASN C 286 ASN D 279 ASN D 286 ASN E 279 ASN E 286 ASN F 279 ASN F 286 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2286 Z= 0.226 Angle : 0.710 4.490 3063 Z= 0.386 Chirality : 0.055 0.169 372 Planarity : 0.004 0.046 381 Dihedral : 8.235 26.596 306 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.26 % Allowed : 14.13 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.37), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.28), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 299 TYR 0.004 0.001 TYR E 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.408 Fit side-chains REVERT: B 314 ASP cc_start: 0.7880 (t0) cc_final: 0.7585 (t70) REVERT: A 317 LYS cc_start: 0.7357 (tptm) cc_final: 0.6746 (pmtt) REVERT: E 321 LYS cc_start: 0.7604 (mtmm) cc_final: 0.7251 (pmtt) REVERT: F 321 LYS cc_start: 0.7133 (mtmt) cc_final: 0.6623 (mmtt) outliers start: 9 outliers final: 5 residues processed: 44 average time/residue: 1.4414 time to fit residues: 65.8044 Evaluate side-chains 38 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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: 0.8092 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2286 Z= 0.185 Angle : 0.575 3.783 3063 Z= 0.305 Chirality : 0.054 0.160 372 Planarity : 0.004 0.042 381 Dihedral : 7.138 22.419 306 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.62 % Allowed : 13.77 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.36), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.27), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 299 TYR 0.002 0.001 TYR F 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 0.400 Fit side-chains REVERT: B 314 ASP cc_start: 0.8042 (t0) cc_final: 0.7751 (t70) REVERT: A 317 LYS cc_start: 0.7351 (tptm) cc_final: 0.6808 (pmtt) REVERT: E 321 LYS cc_start: 0.7606 (mtmm) cc_final: 0.7278 (pmtt) REVERT: F 321 LYS cc_start: 0.7143 (mtmt) cc_final: 0.6627 (mmtt) outliers start: 10 outliers final: 7 residues processed: 39 average time/residue: 1.3779 time to fit residues: 55.9636 Evaluate side-chains 37 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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: 0.8114 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2286 Z= 0.231 Angle : 0.567 3.685 3063 Z= 0.302 Chirality : 0.053 0.157 372 Planarity : 0.004 0.042 381 Dihedral : 7.009 22.418 306 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.07 % Allowed : 12.32 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.36), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.27), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 299 TYR 0.002 0.001 TYR F 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 30 time to evaluate : 0.440 Fit side-chains REVERT: B 314 ASP cc_start: 0.8049 (t0) cc_final: 0.7747 (t70) REVERT: A 317 LYS cc_start: 0.7390 (tptm) cc_final: 0.6894 (pmtt) REVERT: D 282 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7746 (mp) REVERT: E 321 LYS cc_start: 0.7685 (mtmm) cc_final: 0.7349 (pmtt) REVERT: F 321 LYS cc_start: 0.7092 (mtmt) cc_final: 0.6603 (mmmt) outliers start: 14 outliers final: 7 residues processed: 39 average time/residue: 1.2977 time to fit residues: 52.9534 Evaluate side-chains 38 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 30 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.0670 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 overall best weight: 0.6522 ------------------------------------------------------------------------------- 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: 0.8080 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2286 Z= 0.122 Angle : 0.489 3.430 3063 Z= 0.257 Chirality : 0.054 0.151 372 Planarity : 0.003 0.036 381 Dihedral : 6.430 19.684 306 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.54 % Allowed : 14.86 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.36), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.27), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 299 TYR 0.002 0.000 TYR C 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.444 Fit side-chains REVERT: B 282 LEU cc_start: 0.8018 (mp) cc_final: 0.7784 (mm) REVERT: B 314 ASP cc_start: 0.8089 (t0) cc_final: 0.7796 (t70) REVERT: A 317 LYS cc_start: 0.7284 (tptm) cc_final: 0.6802 (pmtt) REVERT: E 321 LYS cc_start: 0.7659 (mtmm) cc_final: 0.7308 (pmtt) outliers start: 7 outliers final: 2 residues processed: 35 average time/residue: 1.5617 time to fit residues: 56.8349 Evaluate side-chains 31 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain F residue 282 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 GLN E 276 GLN F 276 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2286 Z= 0.215 Angle : 0.524 3.525 3063 Z= 0.276 Chirality : 0.053 0.149 372 Planarity : 0.004 0.040 381 Dihedral : 6.531 20.503 306 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.54 % Allowed : 14.86 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.35), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.27), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 299 TYR 0.002 0.001 TYR F 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 29 time to evaluate : 0.446 Fit side-chains REVERT: B 282 LEU cc_start: 0.8059 (mp) cc_final: 0.7819 (mm) REVERT: B 314 ASP cc_start: 0.8062 (t0) cc_final: 0.7781 (t70) REVERT: A 317 LYS cc_start: 0.7411 (tptm) cc_final: 0.6903 (pmtt) REVERT: E 321 LYS cc_start: 0.7658 (mtmm) cc_final: 0.7301 (pmtt) outliers start: 7 outliers final: 5 residues processed: 34 average time/residue: 1.2843 time to fit residues: 45.7518 Evaluate side-chains 34 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 GLN E 276 GLN F 276 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2286 Z= 0.131 Angle : 0.484 3.405 3063 Z= 0.252 Chirality : 0.053 0.143 372 Planarity : 0.003 0.039 381 Dihedral : 6.216 19.159 306 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.45 % Allowed : 15.94 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.36), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.27), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 299 TYR 0.001 0.000 TYR E 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.428 Fit side-chains REVERT: B 282 LEU cc_start: 0.8048 (mp) cc_final: 0.7834 (mm) REVERT: B 314 ASP cc_start: 0.8067 (t0) cc_final: 0.7791 (t70) REVERT: A 317 LYS cc_start: 0.7357 (tptm) cc_final: 0.6894 (pmtt) REVERT: E 321 LYS cc_start: 0.7645 (mtmm) cc_final: 0.7262 (pmtt) outliers start: 4 outliers final: 3 residues processed: 32 average time/residue: 1.3720 time to fit residues: 45.9530 Evaluate side-chains 32 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.0970 chunk 24 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 GLN E 276 GLN F 276 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2286 Z= 0.146 Angle : 0.484 3.437 3063 Z= 0.251 Chirality : 0.053 0.141 372 Planarity : 0.004 0.043 381 Dihedral : 6.093 18.566 306 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.90 % Allowed : 14.49 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.36), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.27), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 299 TYR 0.002 0.000 TYR F 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 29 time to evaluate : 0.420 Fit side-chains REVERT: B 282 LEU cc_start: 0.8053 (mp) cc_final: 0.7847 (mm) REVERT: B 314 ASP cc_start: 0.8075 (t0) cc_final: 0.7799 (t70) REVERT: A 317 LYS cc_start: 0.7391 (tptm) cc_final: 0.6903 (pmtt) REVERT: E 321 LYS cc_start: 0.7628 (mtmm) cc_final: 0.7252 (pmtt) outliers start: 8 outliers final: 5 residues processed: 35 average time/residue: 1.2505 time to fit residues: 45.8649 Evaluate side-chains 34 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 19 optimal weight: 0.0050 chunk 3 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 GLN E 276 GLN F 276 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2286 Z= 0.116 Angle : 0.475 4.019 3063 Z= 0.242 Chirality : 0.054 0.139 372 Planarity : 0.003 0.043 381 Dihedral : 5.901 17.497 306 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.81 % Allowed : 15.58 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.36), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.28), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 299 TYR 0.001 0.000 TYR C 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.406 Fit side-chains REVERT: B 314 ASP cc_start: 0.8093 (t0) cc_final: 0.7817 (t70) REVERT: A 317 LYS cc_start: 0.7365 (tptm) cc_final: 0.6889 (pmtt) REVERT: E 321 LYS cc_start: 0.7618 (mtmm) cc_final: 0.7231 (pmtt) outliers start: 5 outliers final: 3 residues processed: 33 average time/residue: 1.4470 time to fit residues: 49.7200 Evaluate side-chains 32 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain D residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 GLN E 276 GLN F 276 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2286 Z= 0.162 Angle : 0.498 4.359 3063 Z= 0.255 Chirality : 0.053 0.139 372 Planarity : 0.004 0.043 381 Dihedral : 6.007 18.476 306 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.54 % Allowed : 15.58 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.36), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.27), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 299 TYR 0.002 0.001 TYR F 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 29 time to evaluate : 0.438 Fit side-chains REVERT: B 314 ASP cc_start: 0.8087 (t0) cc_final: 0.7812 (t70) REVERT: A 317 LYS cc_start: 0.7398 (tptm) cc_final: 0.6907 (pmtt) REVERT: E 321 LYS cc_start: 0.7624 (mtmm) cc_final: 0.7235 (pmtt) outliers start: 7 outliers final: 5 residues processed: 33 average time/residue: 1.3102 time to fit residues: 45.2722 Evaluate side-chains 34 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 GLN E 276 GLN F 276 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.139573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.128710 restraints weight = 8356.715| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 1.53 r_work: 0.4060 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3990 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2286 Z= 0.127 Angle : 0.477 4.121 3063 Z= 0.244 Chirality : 0.053 0.137 372 Planarity : 0.004 0.042 381 Dihedral : 5.906 17.907 306 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.17 % Allowed : 15.58 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.36), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.28), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 299 TYR 0.001 0.000 TYR F 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3029.13 seconds wall clock time: 53 minutes 41.96 seconds (3221.96 seconds total)