Starting phenix.real_space_refine on Thu Jul 18 19:40:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhr_36285/07_2024/8jhr_36285.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhr_36285/07_2024/8jhr_36285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhr_36285/07_2024/8jhr_36285.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhr_36285/07_2024/8jhr_36285.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhr_36285/07_2024/8jhr_36285.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhr_36285/07_2024/8jhr_36285.cif" } resolution = 3.52 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= -0.002 sd= 0.048 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 19 5.16 5 C 2166 2.51 5 N 548 2.21 5 O 569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 118": "OD1" <-> "OD2" Residue "A ASP 220": "OD1" <-> "OD2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3302 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3277 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 14, 'TRANS': 415} Chain breaks: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'YUX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.76, per 1000 atoms: 0.84 Number of scatterers: 3302 At special positions: 0 Unit cell: (85.85, 60.35, 66.3, 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 19 16.00 O 569 8.00 N 548 7.00 C 2166 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: 2.04 Conformation dependent library (CDL) restraints added in 975.9 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 90.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 98 through 134 removed outlier: 4.753A pdb=" N VAL A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LEU A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASP A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 165 removed outlier: 3.578A pdb=" N ALA A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 167 through 186 removed outlier: 3.819A pdb=" N SER A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 222 Proline residue: A 215 - end of helix removed outlier: 4.163A pdb=" N PHE A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 236 through 257 removed outlier: 3.759A pdb=" N LEU A 240 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 243 " --> pdb=" O PRO A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 264 removed outlier: 3.521A pdb=" N TRP A 261 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 280 removed outlier: 4.388A pdb=" N LEU A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 311 removed outlier: 3.867A pdb=" N ARG A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 350 Proline residue: A 337 - end of helix removed outlier: 4.422A pdb=" N ALA A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 361 removed outlier: 3.689A pdb=" N LYS A 361 " --> pdb=" O CYS A 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 358 through 361' Processing helix chain 'A' and resid 362 through 389 removed outlier: 4.050A pdb=" N PHE A 375 " --> pdb=" O CYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 418 removed outlier: 3.527A pdb=" N LEU A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 416 " --> pdb=" O CYS A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 438 removed outlier: 3.753A pdb=" N ALA A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 451 removed outlier: 3.669A pdb=" N ALA A 444 " --> pdb=" O TRP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 468 Processing helix chain 'A' and resid 474 through 490 removed outlier: 3.545A pdb=" N THR A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 506 Processing helix chain 'A' and resid 506 through 537 removed outlier: 4.435A pdb=" N PHE A 510 " --> pdb=" O MET A 506 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) 281 hydrogen bonds defined for protein. 834 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: 0.95 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1004 1.34 - 1.46: 626 1.46 - 1.58: 1717 1.58 - 1.69: 5 1.69 - 1.81: 28 Bond restraints: 3380 Sorted by residual: bond pdb=" C07 YUX A 601 " pdb=" C08 YUX A 601 " ideal model delta sigma weight residual 1.460 1.611 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" C04 YUX A 601 " pdb=" C05 YUX A 601 " ideal model delta sigma weight residual 1.481 1.591 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C11 YUX A 601 " pdb=" C12 YUX A 601 " ideal model delta sigma weight residual 1.500 1.592 -0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C07 YUX A 601 " pdb=" N06 YUX A 601 " ideal model delta sigma weight residual 1.367 1.452 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C05 YUX A 601 " pdb=" N06 YUX A 601 " ideal model delta sigma weight residual 1.291 1.364 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 3375 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.84: 57 105.84 - 112.91: 1815 112.91 - 119.98: 1218 119.98 - 127.05: 1460 127.05 - 134.12: 41 Bond angle restraints: 4591 Sorted by residual: angle pdb=" N VAL A 265 " pdb=" CA VAL A 265 " pdb=" C VAL A 265 " ideal model delta sigma weight residual 113.53 109.84 3.69 9.80e-01 1.04e+00 1.42e+01 angle pdb=" C THR A 352 " pdb=" N CYS A 353 " pdb=" CA CYS A 353 " ideal model delta sigma weight residual 121.54 128.15 -6.61 1.91e+00 2.74e-01 1.20e+01 angle pdb=" N GLU A 351 " pdb=" CA GLU A 351 " pdb=" C GLU A 351 " ideal model delta sigma weight residual 113.18 108.89 4.29 1.33e+00 5.65e-01 1.04e+01 angle pdb=" C GLY A 162 " pdb=" N ASP A 163 " pdb=" CA ASP A 163 " ideal model delta sigma weight residual 121.14 115.63 5.51 1.75e+00 3.27e-01 9.93e+00 angle pdb=" C ASP A 163 " pdb=" N ARG A 164 " pdb=" CA ARG A 164 " ideal model delta sigma weight residual 122.09 116.49 5.60 1.79e+00 3.12e-01 9.78e+00 ... (remaining 4586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 1664 17.82 - 35.65: 206 35.65 - 53.47: 60 53.47 - 71.30: 12 71.30 - 89.12: 4 Dihedral angle restraints: 1946 sinusoidal: 725 harmonic: 1221 Sorted by residual: dihedral pdb=" CA ALA A 350 " pdb=" C ALA A 350 " pdb=" N GLU A 351 " pdb=" CA GLU A 351 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CG ARG A 299 " pdb=" CD ARG A 299 " pdb=" NE ARG A 299 " pdb=" CZ ARG A 299 " ideal model delta sinusoidal sigma weight residual -180.00 -136.42 -43.58 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CG ARG A 138 " pdb=" CD ARG A 138 " pdb=" NE ARG A 138 " pdb=" CZ ARG A 138 " ideal model delta sinusoidal sigma weight residual 180.00 137.91 42.09 2 1.50e+01 4.44e-03 9.58e+00 ... (remaining 1943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 441 0.054 - 0.107: 78 0.107 - 0.161: 14 0.161 - 0.214: 1 0.214 - 0.268: 3 Chirality restraints: 537 Sorted by residual: chirality pdb=" CG LEU A 413 " pdb=" CB LEU A 413 " pdb=" CD1 LEU A 413 " pdb=" CD2 LEU A 413 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CG LEU A 499 " pdb=" CB LEU A 499 " pdb=" CD1 LEU A 499 " pdb=" CD2 LEU A 499 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB THR A 373 " pdb=" CA THR A 373 " pdb=" OG1 THR A 373 " pdb=" CG2 THR A 373 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 534 not shown) Planarity restraints: 563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 178 " -0.015 2.00e-02 2.50e+03 1.44e-02 5.16e+00 pdb=" CG TRP A 178 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP A 178 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 178 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 178 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 178 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 178 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 136 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C LYS A 136 " 0.032 2.00e-02 2.50e+03 pdb=" O LYS A 136 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP A 137 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 214 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 215 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " 0.024 5.00e-02 4.00e+02 ... (remaining 560 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 420 2.75 - 3.28: 3494 3.28 - 3.82: 5686 3.82 - 4.36: 5948 4.36 - 4.90: 10785 Nonbonded interactions: 26333 Sorted by model distance: nonbonded pdb=" O VAL A 346 " pdb=" OG1 THR A 349 " model vdw 2.208 2.440 nonbonded pdb=" O VAL A 537 " pdb=" ND2 ASN A 538 " model vdw 2.270 2.520 nonbonded pdb=" O MET A 448 " pdb=" NH1 ARG A 456 " model vdw 2.278 2.520 nonbonded pdb=" O ILE A 213 " pdb=" OG1 THR A 216 " model vdw 2.282 2.440 nonbonded pdb=" O TRP A 178 " pdb=" OG1 THR A 182 " model vdw 2.297 2.440 ... (remaining 26328 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.780 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.007 0.151 3380 Z= 0.497 Angle : 0.744 9.441 4591 Z= 0.385 Chirality : 0.046 0.268 537 Planarity : 0.004 0.043 563 Dihedral : 17.688 89.123 1166 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.29 % Allowed : 35.26 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.42), residues: 426 helix: 1.60 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.44 (0.90), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 178 HIS 0.002 0.001 HIS A 132 PHE 0.010 0.001 PHE A 151 TYR 0.006 0.001 TYR A 246 ARG 0.002 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.385 Fit side-chains REVERT: A 306 MET cc_start: 0.8527 (mmm) cc_final: 0.7927 (mmm) outliers start: 1 outliers final: 1 residues processed: 63 average time/residue: 0.1682 time to fit residues: 12.8276 Evaluate side-chains 64 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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: 0.8072 moved from start: 0.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3380 Z= 0.198 Angle : 0.575 6.182 4591 Z= 0.306 Chirality : 0.041 0.173 537 Planarity : 0.004 0.039 563 Dihedral : 6.600 49.777 479 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.62 % Allowed : 30.92 % Favored : 64.45 % 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: 2.16 (0.43), residues: 426 helix: 1.80 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -1.08 (0.98), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 178 HIS 0.001 0.001 HIS A 132 PHE 0.021 0.001 PHE A 510 TYR 0.026 0.001 TYR A 160 ARG 0.001 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 0.330 Fit side-chains REVERT: A 532 ARG cc_start: 0.9126 (tpp80) cc_final: 0.8868 (tpp80) outliers start: 16 outliers final: 10 residues processed: 87 average time/residue: 0.1575 time to fit residues: 16.5378 Evaluate side-chains 80 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 499 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3380 Z= 0.188 Angle : 0.565 6.491 4591 Z= 0.300 Chirality : 0.041 0.189 537 Planarity : 0.004 0.037 563 Dihedral : 6.234 45.973 479 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 6.07 % Allowed : 30.92 % Favored : 63.01 % 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: 2.29 (0.43), residues: 426 helix: 1.87 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.89 (1.00), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 178 HIS 0.001 0.001 HIS A 132 PHE 0.010 0.001 PHE A 151 TYR 0.014 0.001 TYR A 160 ARG 0.001 0.000 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 191 GLN cc_start: 0.6918 (mp-120) cc_final: 0.6716 (mp10) REVERT: A 332 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8494 (mm) REVERT: A 532 ARG cc_start: 0.9111 (tpp80) cc_final: 0.8859 (tpp80) outliers start: 21 outliers final: 14 residues processed: 88 average time/residue: 0.1318 time to fit residues: 14.3011 Evaluate side-chains 78 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8083 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3380 Z= 0.209 Angle : 0.570 6.580 4591 Z= 0.305 Chirality : 0.041 0.198 537 Planarity : 0.004 0.035 563 Dihedral : 6.154 46.584 479 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.78 % Allowed : 30.06 % Favored : 64.16 % 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: 2.23 (0.43), residues: 426 helix: 1.80 (0.28), residues: 374 sheet: None (None), residues: 0 loop : -0.74 (1.04), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 178 HIS 0.001 0.001 HIS A 260 PHE 0.027 0.001 PHE A 510 TYR 0.007 0.001 TYR A 120 ARG 0.002 0.000 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 0.392 Fit side-chains REVERT: A 332 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8521 (mm) REVERT: A 532 ARG cc_start: 0.9125 (tpp80) cc_final: 0.8882 (tpp80) outliers start: 20 outliers final: 14 residues processed: 85 average time/residue: 0.1549 time to fit residues: 15.9093 Evaluate side-chains 77 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 520 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3380 Z= 0.183 Angle : 0.587 8.466 4591 Z= 0.306 Chirality : 0.041 0.202 537 Planarity : 0.004 0.040 563 Dihedral : 6.046 51.581 479 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 6.94 % Allowed : 29.48 % Favored : 63.58 % 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: 2.28 (0.43), residues: 426 helix: 1.83 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.75 (1.03), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 178 HIS 0.001 0.001 HIS A 132 PHE 0.010 0.001 PHE A 327 TYR 0.015 0.001 TYR A 160 ARG 0.003 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 74 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8233 (tt) REVERT: A 315 TYR cc_start: 0.7574 (t80) cc_final: 0.7142 (t80) REVERT: A 332 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8491 (mm) REVERT: A 532 ARG cc_start: 0.9114 (tpp80) cc_final: 0.8904 (tpp80) outliers start: 24 outliers final: 16 residues processed: 91 average time/residue: 0.1448 time to fit residues: 16.1852 Evaluate side-chains 78 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.0980 chunk 10 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 4 optimal weight: 0.0170 chunk 23 optimal weight: 0.9980 overall best weight: 0.3618 ------------------------------------------------------------------------------- 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: 0.8030 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3380 Z= 0.169 Angle : 0.577 7.522 4591 Z= 0.302 Chirality : 0.040 0.168 537 Planarity : 0.004 0.033 563 Dihedral : 5.991 57.973 479 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 5.49 % Allowed : 32.37 % Favored : 62.14 % 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: 2.36 (0.43), residues: 426 helix: 1.91 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -0.85 (1.01), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 178 HIS 0.001 0.001 HIS A 132 PHE 0.032 0.001 PHE A 510 TYR 0.012 0.001 TYR A 192 ARG 0.002 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8209 (tt) REVERT: A 315 TYR cc_start: 0.7554 (t80) cc_final: 0.7156 (t80) REVERT: A 332 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8483 (mm) outliers start: 19 outliers final: 15 residues processed: 78 average time/residue: 0.1704 time to fit residues: 15.9564 Evaluate side-chains 77 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 0.0770 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.0970 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3380 Z= 0.176 Angle : 0.590 7.023 4591 Z= 0.309 Chirality : 0.041 0.157 537 Planarity : 0.005 0.057 563 Dihedral : 5.800 53.340 479 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.49 % Allowed : 32.37 % Favored : 62.14 % 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: 2.39 (0.43), residues: 426 helix: 1.92 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.79 (1.02), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 178 HIS 0.001 0.001 HIS A 132 PHE 0.010 0.001 PHE A 151 TYR 0.016 0.001 TYR A 160 ARG 0.006 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 64 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8250 (tt) REVERT: A 315 TYR cc_start: 0.7483 (t80) cc_final: 0.7098 (t80) REVERT: A 332 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8479 (mm) REVERT: A 462 LEU cc_start: 0.7949 (tp) cc_final: 0.7720 (tp) outliers start: 19 outliers final: 15 residues processed: 77 average time/residue: 0.1516 time to fit residues: 14.4414 Evaluate side-chains 76 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.1980 chunk 20 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 0.0570 chunk 30 optimal weight: 0.8980 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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: 0.8028 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3380 Z= 0.181 Angle : 0.605 8.621 4591 Z= 0.313 Chirality : 0.041 0.151 537 Planarity : 0.004 0.040 563 Dihedral : 5.227 44.009 477 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 6.94 % Allowed : 31.79 % Favored : 61.27 % 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: 2.40 (0.43), residues: 426 helix: 1.92 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.69 (1.04), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 178 HIS 0.001 0.001 HIS A 132 PHE 0.033 0.001 PHE A 510 TYR 0.011 0.001 TYR A 192 ARG 0.005 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 61 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8250 (tt) REVERT: A 315 TYR cc_start: 0.7486 (t80) cc_final: 0.7097 (t80) REVERT: A 332 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8477 (mm) REVERT: A 462 LEU cc_start: 0.7899 (tp) cc_final: 0.7699 (tp) outliers start: 24 outliers final: 17 residues processed: 78 average time/residue: 0.1454 time to fit residues: 14.0123 Evaluate side-chains 76 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 57 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 30.0000 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8068 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3380 Z= 0.222 Angle : 0.614 6.924 4591 Z= 0.324 Chirality : 0.042 0.148 537 Planarity : 0.004 0.040 563 Dihedral : 5.120 43.386 477 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 6.07 % Allowed : 32.08 % Favored : 61.85 % 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: 2.27 (0.43), residues: 426 helix: 1.84 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.75 (1.04), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 178 HIS 0.001 0.001 HIS A 341 PHE 0.012 0.001 PHE A 327 TYR 0.019 0.002 TYR A 160 ARG 0.003 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 62 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8284 (tt) REVERT: A 315 TYR cc_start: 0.7535 (t80) cc_final: 0.7036 (t80) REVERT: A 332 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8482 (mm) outliers start: 21 outliers final: 17 residues processed: 77 average time/residue: 0.1474 time to fit residues: 14.1378 Evaluate side-chains 79 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.0060 chunk 14 optimal weight: 0.5980 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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: 0.8048 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3380 Z= 0.197 Angle : 0.633 8.094 4591 Z= 0.326 Chirality : 0.043 0.235 537 Planarity : 0.004 0.034 563 Dihedral : 4.889 43.827 477 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 5.49 % Allowed : 33.53 % Favored : 60.98 % 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: 2.29 (0.43), residues: 426 helix: 1.85 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.77 (1.01), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 178 HIS 0.001 0.001 HIS A 260 PHE 0.031 0.001 PHE A 510 TYR 0.010 0.001 TYR A 192 ARG 0.004 0.000 ARG A 455 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 59 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8277 (tt) REVERT: A 315 TYR cc_start: 0.7544 (t80) cc_final: 0.7064 (t80) REVERT: A 332 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8472 (mm) outliers start: 19 outliers final: 17 residues processed: 72 average time/residue: 0.1358 time to fit residues: 12.2816 Evaluate side-chains 77 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 58 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.0030 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.160107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.131520 restraints weight = 4865.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.135488 restraints weight = 2731.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.138079 restraints weight = 1919.298| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3380 Z= 0.196 Angle : 0.634 7.463 4591 Z= 0.328 Chirality : 0.043 0.210 537 Planarity : 0.004 0.032 563 Dihedral : 4.779 43.901 477 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.78 % Allowed : 33.53 % Favored : 60.69 % 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: 2.29 (0.43), residues: 426 helix: 1.86 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.84 (0.98), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 178 HIS 0.001 0.001 HIS A 260 PHE 0.010 0.001 PHE A 151 TYR 0.024 0.001 TYR A 160 ARG 0.004 0.000 ARG A 455 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1102.21 seconds wall clock time: 21 minutes 18.06 seconds (1278.06 seconds total)