Starting phenix.real_space_refine on Fri Dec 27 05:47:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thr_41269/12_2024/8thr_41269.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thr_41269/12_2024/8thr_41269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8thr_41269/12_2024/8thr_41269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thr_41269/12_2024/8thr_41269.map" model { file = "/net/cci-nas-00/data/ceres_data/8thr_41269/12_2024/8thr_41269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thr_41269/12_2024/8thr_41269.cif" } resolution = 3.12 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= 0.027 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 28 5.16 5 C 1954 2.51 5 N 454 2.21 5 O 501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 2937 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 2914 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'EBZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.32, per 1000 atoms: 1.13 Number of scatterers: 2937 At special positions: 0 Unit cell: (56.936, 71.817, 75.699, 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 28 16.00 O 501 8.00 N 454 7.00 C 1954 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 380.9 milliseconds 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 702 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 0 sheets defined 89.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 17 through 40 removed outlier: 4.139A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 47 Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 128 through 157 removed outlier: 3.586A pdb=" N LEU A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.942A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 177 removed outlier: 3.811A pdb=" N MET A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 211 removed outlier: 3.574A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 202 " --> pdb=" O CYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.750A pdb=" N GLY A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 249 through 270 removed outlier: 3.929A pdb=" N LEU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 255 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.743A pdb=" N LEU A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 312 removed outlier: 3.753A pdb=" N LEU A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.900A pdb=" N THR A 322 " --> pdb=" O MET A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 334 through 356 removed outlier: 3.911A pdb=" N LEU A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 373 removed outlier: 3.577A pdb=" N GLY A 364 " --> pdb=" O CYS A 360 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 380 through 383 Processing helix chain 'A' and resid 384 through 414 Proline residue: A 404 - end of helix removed outlier: 3.834A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 436 removed outlier: 4.293A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 removed outlier: 4.144A pdb=" N ALA A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 445' Processing helix chain 'A' and resid 448 through 462 removed outlier: 3.944A pdb=" N LEU A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP A 460 " --> pdb=" O ILE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 removed outlier: 3.642A pdb=" N CYS A 467 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 469 " --> pdb=" O LEU A 466 " (cutoff:3.500A) 207 hydrogen bonds defined for protein. 582 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: 0.78 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 498 1.32 - 1.45: 745 1.45 - 1.57: 1716 1.57 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 3007 Sorted by residual: bond pdb=" CA VAL A 220 " pdb=" CB VAL A 220 " ideal model delta sigma weight residual 1.539 1.491 0.049 1.20e-02 6.94e+03 1.65e+01 bond pdb=" N PRO A 437 " pdb=" CD PRO A 437 " ideal model delta sigma weight residual 1.473 1.427 0.046 1.40e-02 5.10e+03 1.09e+01 bond pdb=" N PRO A 313 " pdb=" CD PRO A 313 " ideal model delta sigma weight residual 1.473 1.428 0.045 1.40e-02 5.10e+03 1.02e+01 bond pdb=" CA TYR A 418 " pdb=" CB TYR A 418 " ideal model delta sigma weight residual 1.530 1.484 0.046 1.51e-02 4.39e+03 9.44e+00 bond pdb=" CB THR A 140 " pdb=" OG1 THR A 140 " ideal model delta sigma weight residual 1.433 1.385 0.048 1.60e-02 3.91e+03 8.97e+00 ... (remaining 3002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 2899 1.88 - 3.76: 972 3.76 - 5.63: 183 5.63 - 7.51: 29 7.51 - 9.39: 7 Bond angle restraints: 4090 Sorted by residual: angle pdb=" N MET A 319 " pdb=" CA MET A 319 " pdb=" C MET A 319 " ideal model delta sigma weight residual 111.40 118.41 -7.01 1.22e+00 6.72e-01 3.30e+01 angle pdb=" N VAL A 427 " pdb=" CA VAL A 427 " pdb=" CB VAL A 427 " ideal model delta sigma weight residual 110.54 118.23 -7.69 1.36e+00 5.41e-01 3.20e+01 angle pdb=" N SER A 420 " pdb=" CA SER A 420 " pdb=" C SER A 420 " ideal model delta sigma weight residual 112.04 120.07 -8.03 1.44e+00 4.82e-01 3.11e+01 angle pdb=" CA ILE A 455 " pdb=" C ILE A 455 " pdb=" N ILE A 456 " ideal model delta sigma weight residual 117.28 123.73 -6.45 1.16e+00 7.43e-01 3.09e+01 angle pdb=" CA ASN A 154 " pdb=" CB ASN A 154 " pdb=" CG ASN A 154 " ideal model delta sigma weight residual 112.60 118.14 -5.54 1.00e+00 1.00e+00 3.07e+01 ... (remaining 4085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 1616 16.30 - 32.60: 141 32.60 - 48.90: 25 48.90 - 65.19: 7 65.19 - 81.49: 1 Dihedral angle restraints: 1790 sinusoidal: 689 harmonic: 1101 Sorted by residual: dihedral pdb=" CA CYS A 360 " pdb=" C CYS A 360 " pdb=" N ALA A 361 " pdb=" CA ALA A 361 " ideal model delta harmonic sigma weight residual 180.00 153.16 26.84 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ILE A 156 " pdb=" C ILE A 156 " pdb=" N GLY A 157 " pdb=" CA GLY A 157 " ideal model delta harmonic sigma weight residual 180.00 -155.51 -24.49 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ASN A 128 " pdb=" C ASN A 128 " pdb=" N VAL A 129 " pdb=" CA VAL A 129 " ideal model delta harmonic sigma weight residual -180.00 -156.54 -23.46 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 1787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 288 0.089 - 0.179: 155 0.179 - 0.268: 34 0.268 - 0.358: 8 0.358 - 0.447: 2 Chirality restraints: 487 Sorted by residual: chirality pdb=" CA SER A 420 " pdb=" N SER A 420 " pdb=" C SER A 420 " pdb=" CB SER A 420 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" CA LEU A 152 " pdb=" N LEU A 152 " pdb=" C LEU A 152 " pdb=" CB LEU A 152 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB THR A 140 " pdb=" CA THR A 140 " pdb=" OG1 THR A 140 " pdb=" CG2 THR A 140 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 484 not shown) Planarity restraints: 501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 176 " 0.112 2.00e-02 2.50e+03 7.03e-02 8.64e+01 pdb=" CG PHE A 176 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE A 176 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 PHE A 176 " -0.072 2.00e-02 2.50e+03 pdb=" CE1 PHE A 176 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 176 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 176 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 EBZ A 601 " -0.062 2.00e-02 2.50e+03 5.00e-02 6.24e+01 pdb=" C06 EBZ A 601 " -0.039 2.00e-02 2.50e+03 pdb=" C07 EBZ A 601 " -0.019 2.00e-02 2.50e+03 pdb=" C09 EBZ A 601 " 0.017 2.00e-02 2.50e+03 pdb=" C14 EBZ A 601 " 0.098 2.00e-02 2.50e+03 pdb=" C15 EBZ A 601 " 0.028 2.00e-02 2.50e+03 pdb=" C16 EBZ A 601 " -0.010 2.00e-02 2.50e+03 pdb=" C17 EBZ A 601 " -0.015 2.00e-02 2.50e+03 pdb=" O01 EBZ A 601 " 0.065 2.00e-02 2.50e+03 pdb=" O02 EBZ A 601 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 422 " 0.091 2.00e-02 2.50e+03 4.75e-02 4.51e+01 pdb=" CG TYR A 422 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 422 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR A 422 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR A 422 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 422 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 422 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 422 " 0.064 2.00e-02 2.50e+03 ... (remaining 498 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1517 3.01 - 3.48: 3458 3.48 - 3.95: 4867 3.95 - 4.43: 5561 4.43 - 4.90: 9114 Nonbonded interactions: 24517 Sorted by model distance: nonbonded pdb=" OD1 ASP A 411 " pdb=" OH TYR A 418 " model vdw 2.537 3.040 nonbonded pdb=" O SER A 420 " pdb=" N ALA A 423 " model vdw 2.561 3.120 nonbonded pdb=" N THR A 249 " pdb=" N ALA A 250 " model vdw 2.562 2.560 nonbonded pdb=" O ILE A 455 " pdb=" CA ILE A 456 " model vdw 2.574 2.776 nonbonded pdb=" OD1 ASP A 411 " pdb=" OG SER A 416 " model vdw 2.601 3.040 ... (remaining 24512 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.870 Find NCS groups from input model: 0.020 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 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 : 0.012 0.049 3007 Z= 0.790 Angle : 1.889 9.388 4090 Z= 1.258 Chirality : 0.108 0.447 487 Planarity : 0.014 0.070 501 Dihedral : 13.084 81.492 1088 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.96 % Allowed : 7.03 % Favored : 92.01 % Cbeta Deviations : 0.28 % 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: -3.14 (0.37), residues: 385 helix: -1.94 (0.25), residues: 275 sheet: None (None), residues: 0 loop : -1.95 (0.61), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.016 TRP A 451 HIS 0.003 0.002 HIS A 353 PHE 0.112 0.016 PHE A 176 TYR 0.091 0.015 TYR A 422 ARG 0.004 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 443 ILE cc_start: 0.7773 (mt) cc_final: 0.7455 (mt) outliers start: 3 outliers final: 0 residues processed: 83 average time/residue: 0.1091 time to fit residues: 11.6887 Evaluate side-chains 67 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.0050 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN A 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3007 Z= 0.312 Angle : 0.833 7.929 4090 Z= 0.415 Chirality : 0.048 0.175 487 Planarity : 0.006 0.058 501 Dihedral : 7.460 26.051 441 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.56 % Allowed : 14.70 % Favored : 82.75 % 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: -1.16 (0.43), residues: 385 helix: -0.39 (0.30), residues: 282 sheet: None (None), residues: 0 loop : -1.49 (0.70), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 328 HIS 0.001 0.001 HIS A 414 PHE 0.019 0.002 PHE A 238 TYR 0.015 0.002 TYR A 422 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.316 Fit side-chains REVERT: A 244 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6196 (tt0) REVERT: A 443 ILE cc_start: 0.7786 (mt) cc_final: 0.7427 (mt) outliers start: 8 outliers final: 2 residues processed: 74 average time/residue: 0.0969 time to fit residues: 9.4846 Evaluate side-chains 67 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 339 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 9 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 chunk 37 optimal weight: 0.0670 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3007 Z= 0.254 Angle : 0.771 8.924 4090 Z= 0.378 Chirality : 0.046 0.158 487 Planarity : 0.006 0.061 501 Dihedral : 6.936 26.013 441 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.24 % Allowed : 17.89 % Favored : 79.87 % 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: -0.83 (0.43), residues: 385 helix: -0.09 (0.30), residues: 282 sheet: None (None), residues: 0 loop : -1.58 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 328 HIS 0.002 0.001 HIS A 414 PHE 0.014 0.002 PHE A 238 TYR 0.020 0.002 TYR A 422 ARG 0.001 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.309 Fit side-chains REVERT: A 244 GLU cc_start: 0.6595 (tt0) cc_final: 0.6367 (tt0) REVERT: A 288 LEU cc_start: 0.8124 (mt) cc_final: 0.7898 (mp) REVERT: A 323 MET cc_start: 0.6258 (ppp) cc_final: 0.5637 (ppp) REVERT: A 324 CYS cc_start: 0.3439 (p) cc_final: 0.3211 (m) REVERT: A 443 ILE cc_start: 0.7733 (mt) cc_final: 0.7400 (mt) outliers start: 7 outliers final: 3 residues processed: 72 average time/residue: 0.1032 time to fit residues: 9.7991 Evaluate side-chains 69 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 306 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7154 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3007 Z= 0.353 Angle : 0.811 7.524 4090 Z= 0.396 Chirality : 0.048 0.165 487 Planarity : 0.006 0.066 501 Dihedral : 6.888 24.272 441 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.19 % Allowed : 21.73 % Favored : 75.08 % 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: -0.97 (0.42), residues: 385 helix: -0.19 (0.29), residues: 286 sheet: None (None), residues: 0 loop : -1.67 (0.68), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.003 0.001 HIS A 414 PHE 0.015 0.002 PHE A 178 TYR 0.020 0.003 TYR A 422 ARG 0.002 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.313 Fit side-chains REVERT: A 288 LEU cc_start: 0.8167 (mt) cc_final: 0.7960 (mp) REVERT: A 443 ILE cc_start: 0.7855 (mt) cc_final: 0.7488 (mt) outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.1041 time to fit residues: 9.2643 Evaluate side-chains 71 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 395 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 0.0050 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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: 0.7096 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3007 Z= 0.247 Angle : 0.757 8.996 4090 Z= 0.365 Chirality : 0.045 0.147 487 Planarity : 0.006 0.064 501 Dihedral : 6.628 24.284 441 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.83 % Allowed : 20.13 % Favored : 76.04 % 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: -0.66 (0.43), residues: 385 helix: 0.16 (0.30), residues: 279 sheet: None (None), residues: 0 loop : -1.86 (0.63), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 328 HIS 0.002 0.001 HIS A 414 PHE 0.010 0.001 PHE A 238 TYR 0.018 0.002 TYR A 422 ARG 0.001 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.312 Fit side-chains REVERT: A 185 LEU cc_start: 0.5714 (tp) cc_final: 0.5409 (tp) REVERT: A 323 MET cc_start: 0.6216 (ppp) cc_final: 0.5929 (ppp) REVERT: A 405 ILE cc_start: 0.7043 (OUTLIER) cc_final: 0.6601 (mm) outliers start: 12 outliers final: 8 residues processed: 72 average time/residue: 0.0984 time to fit residues: 9.3354 Evaluate side-chains 70 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7123 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3007 Z= 0.296 Angle : 0.777 8.557 4090 Z= 0.376 Chirality : 0.046 0.151 487 Planarity : 0.006 0.065 501 Dihedral : 6.634 23.667 441 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.83 % Allowed : 21.73 % Favored : 74.44 % 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: -0.73 (0.42), residues: 385 helix: 0.15 (0.31), residues: 279 sheet: None (None), residues: 0 loop : -2.02 (0.60), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 358 HIS 0.003 0.001 HIS A 414 PHE 0.011 0.002 PHE A 178 TYR 0.020 0.002 TYR A 422 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.520 Fit side-chains REVERT: A 319 MET cc_start: 0.3885 (mmm) cc_final: 0.3499 (mmp) REVERT: A 355 MET cc_start: 0.6730 (ptp) cc_final: 0.6319 (ptp) REVERT: A 405 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6680 (mm) outliers start: 12 outliers final: 9 residues processed: 74 average time/residue: 0.1221 time to fit residues: 12.2576 Evaluate side-chains 73 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.0040 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 22 optimal weight: 0.0570 chunk 16 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 overall best weight: 0.2710 ------------------------------------------------------------------------------- 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: 0.7071 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3007 Z= 0.218 Angle : 0.738 8.213 4090 Z= 0.353 Chirality : 0.044 0.181 487 Planarity : 0.006 0.063 501 Dihedral : 6.463 23.285 441 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.79 % Allowed : 20.13 % Favored : 75.08 % 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: -0.54 (0.43), residues: 385 helix: 0.30 (0.31), residues: 279 sheet: None (None), residues: 0 loop : -2.00 (0.59), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.024 0.001 PHE A 429 TYR 0.017 0.002 TYR A 422 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.315 Fit side-chains REVERT: A 185 LEU cc_start: 0.5646 (tp) cc_final: 0.5353 (tp) REVERT: A 355 MET cc_start: 0.6608 (ptp) cc_final: 0.6390 (ptp) REVERT: A 405 ILE cc_start: 0.7022 (OUTLIER) cc_final: 0.6567 (mm) outliers start: 15 outliers final: 10 residues processed: 76 average time/residue: 0.1031 time to fit residues: 10.2734 Evaluate side-chains 78 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.0670 chunk 14 optimal weight: 0.4980 chunk 26 optimal weight: 0.0050 chunk 10 optimal weight: 0.5980 overall best weight: 0.3332 ------------------------------------------------------------------------------- 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: 0.7069 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3007 Z= 0.235 Angle : 0.755 8.956 4090 Z= 0.360 Chirality : 0.045 0.182 487 Planarity : 0.006 0.063 501 Dihedral : 6.408 23.229 441 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.47 % Allowed : 19.49 % Favored : 76.04 % 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: -0.40 (0.43), residues: 385 helix: 0.39 (0.31), residues: 282 sheet: None (None), residues: 0 loop : -1.94 (0.61), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.021 0.001 PHE A 429 TYR 0.018 0.002 TYR A 422 ARG 0.002 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.289 Fit side-chains REVERT: A 185 LEU cc_start: 0.5692 (tp) cc_final: 0.5414 (tp) REVERT: A 405 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6612 (mm) REVERT: A 406 MET cc_start: 0.7197 (mpp) cc_final: 0.6888 (mpp) outliers start: 14 outliers final: 9 residues processed: 77 average time/residue: 0.1055 time to fit residues: 10.6422 Evaluate side-chains 76 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7108 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3007 Z= 0.299 Angle : 0.810 10.426 4090 Z= 0.388 Chirality : 0.048 0.188 487 Planarity : 0.006 0.064 501 Dihedral : 6.549 22.894 441 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.79 % Allowed : 21.09 % Favored : 74.12 % 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: -0.57 (0.43), residues: 385 helix: 0.25 (0.31), residues: 282 sheet: None (None), residues: 0 loop : -1.95 (0.62), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 358 HIS 0.003 0.001 HIS A 414 PHE 0.026 0.002 PHE A 348 TYR 0.026 0.003 TYR A 243 ARG 0.001 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.280 Fit side-chains REVERT: A 355 MET cc_start: 0.6403 (OUTLIER) cc_final: 0.5621 (ptp) REVERT: A 405 ILE cc_start: 0.7143 (OUTLIER) cc_final: 0.6727 (mm) outliers start: 15 outliers final: 9 residues processed: 75 average time/residue: 0.1004 time to fit residues: 9.8478 Evaluate side-chains 78 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.0970 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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: 0.7095 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3007 Z= 0.284 Angle : 0.863 11.915 4090 Z= 0.399 Chirality : 0.048 0.197 487 Planarity : 0.006 0.064 501 Dihedral : 6.580 23.329 441 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.83 % Allowed : 22.36 % Favored : 73.80 % 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: -0.52 (0.43), residues: 385 helix: 0.29 (0.31), residues: 282 sheet: None (None), residues: 0 loop : -1.97 (0.61), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 358 HIS 0.003 0.001 HIS A 414 PHE 0.026 0.002 PHE A 348 TYR 0.024 0.002 TYR A 243 ARG 0.001 0.000 ARG A 189 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.290 Fit side-chains REVERT: A 185 LEU cc_start: 0.5875 (tp) cc_final: 0.5597 (tp) REVERT: A 355 MET cc_start: 0.6336 (OUTLIER) cc_final: 0.5644 (ptp) REVERT: A 405 ILE cc_start: 0.7118 (OUTLIER) cc_final: 0.6700 (mm) outliers start: 12 outliers final: 8 residues processed: 73 average time/residue: 0.1188 time to fit residues: 11.3417 Evaluate side-chains 76 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.3980 chunk 1 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 0.0040 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.0970 chunk 14 optimal weight: 0.0980 chunk 37 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 overall best weight: 0.1990 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.147319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.135805 restraints weight = 4904.901| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.31 r_work: 0.3901 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3007 Z= 0.212 Angle : 0.823 11.877 4090 Z= 0.374 Chirality : 0.045 0.198 487 Planarity : 0.006 0.062 501 Dihedral : 6.251 23.005 441 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.83 % Allowed : 22.36 % Favored : 73.80 % 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: -0.23 (0.44), residues: 385 helix: 0.52 (0.31), residues: 283 sheet: None (None), residues: 0 loop : -1.91 (0.62), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 451 HIS 0.002 0.001 HIS A 414 PHE 0.023 0.001 PHE A 348 TYR 0.022 0.002 TYR A 243 ARG 0.002 0.000 ARG A 189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1203.02 seconds wall clock time: 22 minutes 26.93 seconds (1346.93 seconds total)