Starting phenix.real_space_refine on Fri Apr 5 14:54:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtt_36652/04_2024/8jtt_36652_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtt_36652/04_2024/8jtt_36652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtt_36652/04_2024/8jtt_36652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtt_36652/04_2024/8jtt_36652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtt_36652/04_2024/8jtt_36652_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtt_36652/04_2024/8jtt_36652_updated.pdb" } resolution = 3.87 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= 0.001 sd= 0.083 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 21 5.16 5 C 2182 2.51 5 N 534 2.21 5 O 584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 13": "OE1" <-> "OE2" Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3321 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3312 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 113 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'MF8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.43, per 1000 atoms: 0.73 Number of scatterers: 3321 At special positions: 0 Unit cell: (85.5175, 58.455, 64.95, 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 21 16.00 O 584 8.00 N 534 7.00 C 2182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 717.0 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 836 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 0 sheets defined 68.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 16 through 32 removed outlier: 4.061A pdb=" N ALA A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 137 No H-bonds generated for 'chain 'A' and resid 134 through 137' Processing helix chain 'A' and resid 144 through 172 removed outlier: 3.515A pdb=" N LEU A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 Processing helix chain 'A' and resid 199 through 227 Processing helix chain 'A' and resid 230 through 256 removed outlier: 4.182A pdb=" N ARG A 233 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ARG A 234 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR A 235 " --> pdb=" O SER A 232 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 256 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 277 removed outlier: 3.694A pdb=" N LEU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 286 through 292 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 321 through 323 No H-bonds generated for 'chain 'A' and resid 321 through 323' Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 340 through 366 removed outlier: 5.596A pdb=" N LYS A 345 " --> pdb=" O PRO A 341 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ARG A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 Processing helix chain 'A' and resid 385 through 396 removed outlier: 3.749A pdb=" N GLY A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 421 removed outlier: 4.447A pdb=" N VAL A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N MET A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 455 removed outlier: 3.702A pdb=" N CYS A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 469 Processing helix chain 'A' and resid 474 through 490 Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 492 through 509 removed outlier: 3.962A pdb=" N LEU A 496 " --> pdb=" O GLN A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 529 204 hydrogen bonds defined for protein. 555 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: 0.86 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1031 1.34 - 1.46: 712 1.46 - 1.58: 1625 1.58 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 3400 Sorted by residual: bond pdb=" C07 MF8 A 601 " pdb=" N08 MF8 A 601 " ideal model delta sigma weight residual 1.281 1.439 -0.158 2.00e-02 2.50e+03 6.28e+01 bond pdb=" C07 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 1.393 1.252 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C04 MF8 A 601 " pdb=" N02 MF8 A 601 " ideal model delta sigma weight residual 1.362 1.448 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C07 MF8 A 601 " pdb=" N09 MF8 A 601 " ideal model delta sigma weight residual 1.358 1.444 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C04 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 1.387 1.454 -0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 3395 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.28: 100 106.28 - 113.22: 1847 113.22 - 120.16: 1254 120.16 - 127.10: 1415 127.10 - 134.04: 45 Bond angle restraints: 4661 Sorted by residual: angle pdb=" N02 MF8 A 601 " pdb=" C04 MF8 A 601 " pdb=" N05 MF8 A 601 " ideal model delta sigma weight residual 126.24 116.62 9.62 3.00e+00 1.11e-01 1.03e+01 angle pdb=" N02 MF8 A 601 " pdb=" C04 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 113.43 122.89 -9.46 3.00e+00 1.11e-01 9.93e+00 angle pdb=" N ARG A 439 " pdb=" CA ARG A 439 " pdb=" C ARG A 439 " ideal model delta sigma weight residual 111.07 107.88 3.19 1.07e+00 8.73e-01 8.88e+00 angle pdb=" N MET A 448 " pdb=" CA MET A 448 " pdb=" C MET A 448 " ideal model delta sigma weight residual 111.14 113.92 -2.78 1.08e+00 8.57e-01 6.62e+00 angle pdb=" C VAL A 212 " pdb=" CA VAL A 212 " pdb=" CB VAL A 212 " ideal model delta sigma weight residual 112.22 108.70 3.52 1.38e+00 5.25e-01 6.52e+00 ... (remaining 4656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 1766 16.55 - 33.10: 150 33.10 - 49.65: 31 49.65 - 66.20: 0 66.20 - 82.75: 1 Dihedral angle restraints: 1948 sinusoidal: 648 harmonic: 1300 Sorted by residual: dihedral pdb=" CA THR A 396 " pdb=" C THR A 396 " pdb=" N ILE A 397 " pdb=" CA ILE A 397 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA LEU A 521 " pdb=" C LEU A 521 " pdb=" N PRO A 522 " pdb=" CA PRO A 522 " ideal model delta harmonic sigma weight residual 180.00 164.07 15.93 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA LEU A 27 " pdb=" C LEU A 27 " pdb=" N LEU A 28 " pdb=" CA LEU A 28 " ideal model delta harmonic sigma weight residual 180.00 164.52 15.48 0 5.00e+00 4.00e-02 9.59e+00 ... (remaining 1945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 414 0.048 - 0.097: 116 0.097 - 0.145: 29 0.145 - 0.193: 2 0.193 - 0.241: 4 Chirality restraints: 565 Sorted by residual: chirality pdb=" CB THR A 45 " pdb=" CA THR A 45 " pdb=" OG1 THR A 45 " pdb=" CG2 THR A 45 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB VAL A 228 " pdb=" CA VAL A 228 " pdb=" CG1 VAL A 228 " pdb=" CG2 VAL A 228 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL A 166 " pdb=" CA VAL A 166 " pdb=" CG1 VAL A 166 " pdb=" CG2 VAL A 166 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 562 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 MF8 A 601 " -0.222 2.00e-02 2.50e+03 3.51e-01 2.78e+03 pdb=" C03 MF8 A 601 " -0.138 2.00e-02 2.50e+03 pdb=" C04 MF8 A 601 " 0.229 2.00e-02 2.50e+03 pdb=" C07 MF8 A 601 " -0.097 2.00e-02 2.50e+03 pdb=" N02 MF8 A 601 " -0.043 2.00e-02 2.50e+03 pdb=" N05 MF8 A 601 " 0.587 2.00e-02 2.50e+03 pdb=" N06 MF8 A 601 " 0.083 2.00e-02 2.50e+03 pdb=" N08 MF8 A 601 " 0.325 2.00e-02 2.50e+03 pdb=" N09 MF8 A 601 " -0.723 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO A 271 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 282 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO A 283 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " -0.027 5.00e-02 4.00e+02 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 756 2.78 - 3.31: 3322 3.31 - 3.84: 5628 3.84 - 4.37: 5801 4.37 - 4.90: 9930 Nonbonded interactions: 25437 Sorted by model distance: nonbonded pdb=" OG SER A 409 " pdb=" O GLY A 441 " model vdw 2.250 2.440 nonbonded pdb=" O PHE A 22 " pdb=" OH TYR A 240 " model vdw 2.252 2.440 nonbonded pdb=" O LEU A 42 " pdb=" OG SER A 133 " model vdw 2.348 2.440 nonbonded pdb=" OG1 THR A 245 " pdb=" OE1 GLU A 386 " model vdw 2.357 2.440 nonbonded pdb=" O LEU A 487 " pdb=" N TRP A 491 " model vdw 2.364 2.520 ... (remaining 25432 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.840 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.310 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 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 : 0.006 0.158 3400 Z= 0.410 Angle : 0.869 9.617 4661 Z= 0.444 Chirality : 0.049 0.241 565 Planarity : 0.016 0.351 581 Dihedral : 12.926 82.753 1112 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -2.01 (0.35), residues: 450 helix: -0.51 (0.26), residues: 327 sheet: None (None), residues: 0 loop : -3.46 (0.45), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 217 HIS 0.002 0.001 HIS A 367 PHE 0.027 0.002 PHE A 482 TYR 0.015 0.001 TYR A 240 ARG 0.002 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.327 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1012 time to fit residues: 9.8914 Evaluate side-chains 54 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.5854 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3400 Z= 0.181 Angle : 0.576 9.855 4661 Z= 0.295 Chirality : 0.038 0.139 565 Planarity : 0.006 0.051 581 Dihedral : 4.354 16.285 475 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.85 % Allowed : 8.00 % Favored : 90.15 % 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: -0.99 (0.38), residues: 450 helix: 0.36 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -3.55 (0.47), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 261 HIS 0.003 0.001 HIS A 260 PHE 0.009 0.001 PHE A 151 TYR 0.012 0.001 TYR A 199 ARG 0.003 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.345 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 0.1024 time to fit residues: 8.5847 Evaluate side-chains 61 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 461 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.0060 chunk 21 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3400 Z= 0.173 Angle : 0.554 9.474 4661 Z= 0.281 Chirality : 0.037 0.138 565 Planarity : 0.005 0.048 581 Dihedral : 4.182 17.000 475 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.69 % Allowed : 12.92 % Favored : 83.38 % 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: -0.60 (0.40), residues: 450 helix: 0.60 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -3.30 (0.51), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 261 HIS 0.003 0.001 HIS A 260 PHE 0.009 0.001 PHE A 151 TYR 0.010 0.001 TYR A 199 ARG 0.002 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.365 Fit side-chains REVERT: A 403 ILE cc_start: 0.6717 (mm) cc_final: 0.6151 (mm) outliers start: 12 outliers final: 8 residues processed: 65 average time/residue: 0.0948 time to fit residues: 8.6068 Evaluate side-chains 67 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3400 Z= 0.294 Angle : 0.668 9.703 4661 Z= 0.349 Chirality : 0.041 0.168 565 Planarity : 0.005 0.048 581 Dihedral : 4.699 17.544 475 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.00 % Allowed : 17.54 % Favored : 78.46 % 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: -0.79 (0.40), residues: 450 helix: 0.45 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -2.98 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 261 HIS 0.006 0.002 HIS A 260 PHE 0.021 0.002 PHE A 151 TYR 0.011 0.002 TYR A 199 ARG 0.003 0.001 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.317 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 70 average time/residue: 0.1036 time to fit residues: 9.8930 Evaluate side-chains 67 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.0170 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3400 Z= 0.187 Angle : 0.571 9.387 4661 Z= 0.288 Chirality : 0.037 0.149 565 Planarity : 0.004 0.046 581 Dihedral : 4.322 18.260 475 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.62 % Allowed : 20.00 % Favored : 75.38 % 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: -0.55 (0.41), residues: 450 helix: 0.64 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -3.02 (0.54), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 261 HIS 0.003 0.001 HIS A 260 PHE 0.009 0.001 PHE A 151 TYR 0.010 0.001 TYR A 199 ARG 0.002 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.315 Fit side-chains REVERT: A 173 PHE cc_start: 0.4749 (OUTLIER) cc_final: 0.4489 (m-10) outliers start: 15 outliers final: 10 residues processed: 67 average time/residue: 0.1010 time to fit residues: 9.4550 Evaluate side-chains 65 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3400 Z= 0.190 Angle : 0.598 9.607 4661 Z= 0.296 Chirality : 0.037 0.137 565 Planarity : 0.004 0.046 581 Dihedral : 4.219 18.127 475 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.92 % Allowed : 20.62 % Favored : 74.46 % 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: -0.43 (0.41), residues: 450 helix: 0.74 (0.30), residues: 323 sheet: None (None), residues: 0 loop : -3.00 (0.54), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 261 HIS 0.002 0.001 HIS A 367 PHE 0.027 0.001 PHE A 151 TYR 0.009 0.001 TYR A 199 ARG 0.002 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 0.387 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 68 average time/residue: 0.0844 time to fit residues: 8.0992 Evaluate side-chains 70 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 chunk 43 optimal weight: 0.0370 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 0.0870 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5996 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3400 Z= 0.169 Angle : 0.582 9.271 4661 Z= 0.284 Chirality : 0.036 0.118 565 Planarity : 0.004 0.045 581 Dihedral : 4.045 18.532 475 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.38 % Allowed : 22.46 % Favored : 74.15 % 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: -0.17 (0.41), residues: 450 helix: 0.92 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -2.85 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 261 HIS 0.001 0.000 HIS A 367 PHE 0.029 0.001 PHE A 151 TYR 0.008 0.001 TYR A 199 ARG 0.002 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.341 Fit side-chains REVERT: A 371 THR cc_start: 0.4872 (OUTLIER) cc_final: 0.4296 (t) outliers start: 11 outliers final: 10 residues processed: 66 average time/residue: 0.0936 time to fit residues: 9.1453 Evaluate side-chains 66 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.2980 chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 0.0020 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3400 Z= 0.175 Angle : 0.585 9.202 4661 Z= 0.287 Chirality : 0.037 0.119 565 Planarity : 0.004 0.046 581 Dihedral : 4.017 18.388 475 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.62 % Allowed : 23.69 % Favored : 71.69 % 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: -0.12 (0.41), residues: 450 helix: 0.98 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.78 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 261 HIS 0.002 0.001 HIS A 304 PHE 0.029 0.001 PHE A 151 TYR 0.008 0.001 TYR A 199 ARG 0.001 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 58 time to evaluate : 0.340 Fit side-chains REVERT: A 371 THR cc_start: 0.4991 (OUTLIER) cc_final: 0.4412 (t) outliers start: 15 outliers final: 13 residues processed: 68 average time/residue: 0.0886 time to fit residues: 8.4361 Evaluate side-chains 70 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 44 optimal weight: 0.0070 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3400 Z= 0.181 Angle : 0.592 9.180 4661 Z= 0.291 Chirality : 0.037 0.120 565 Planarity : 0.004 0.045 581 Dihedral : 3.993 18.084 475 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.92 % Allowed : 23.69 % Favored : 71.38 % 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: -0.14 (0.41), residues: 450 helix: 0.94 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.73 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 261 HIS 0.002 0.001 HIS A 260 PHE 0.011 0.001 PHE A 22 TYR 0.007 0.001 TYR A 199 ARG 0.002 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 0.345 Fit side-chains REVERT: A 371 THR cc_start: 0.5065 (OUTLIER) cc_final: 0.4477 (t) outliers start: 16 outliers final: 13 residues processed: 68 average time/residue: 0.0931 time to fit residues: 8.9188 Evaluate side-chains 71 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.0000 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3400 Z= 0.181 Angle : 0.597 9.145 4661 Z= 0.294 Chirality : 0.037 0.119 565 Planarity : 0.004 0.046 581 Dihedral : 3.970 18.095 475 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.31 % Allowed : 24.31 % Favored : 71.38 % 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: -0.15 (0.41), residues: 450 helix: 0.92 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -2.72 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 261 HIS 0.001 0.001 HIS A 260 PHE 0.013 0.001 PHE A 22 TYR 0.007 0.001 TYR A 199 ARG 0.002 0.000 ARG A 439 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.315 Fit side-chains REVERT: A 371 THR cc_start: 0.5119 (OUTLIER) cc_final: 0.4548 (t) REVERT: A 455 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6876 (mm-30) outliers start: 14 outliers final: 13 residues processed: 69 average time/residue: 0.0903 time to fit residues: 8.6070 Evaluate side-chains 72 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.0570 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 25 optimal weight: 0.0670 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5388 r_free = 0.5388 target = 0.294681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5181 r_free = 0.5181 target = 0.268705 restraints weight = 3858.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.5214 r_free = 0.5214 target = 0.273772 restraints weight = 2199.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5232 r_free = 0.5232 target = 0.276670 restraints weight = 1521.256| |-----------------------------------------------------------------------------| r_work (final): 0.5252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5962 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3400 Z= 0.167 Angle : 0.593 9.241 4661 Z= 0.290 Chirality : 0.036 0.112 565 Planarity : 0.004 0.045 581 Dihedral : 3.886 17.933 475 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.38 % Allowed : 25.23 % Favored : 71.38 % 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: -0.03 (0.41), residues: 450 helix: 1.02 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -2.71 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 491 HIS 0.001 0.001 HIS A 367 PHE 0.013 0.001 PHE A 22 TYR 0.006 0.001 TYR A 199 ARG 0.001 0.000 ARG A 439 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1056.08 seconds wall clock time: 19 minutes 46.76 seconds (1186.76 seconds total)