Starting phenix.real_space_refine on Fri Apr 5 13:33:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t69_41066/04_2024/8t69_41066_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t69_41066/04_2024/8t69_41066.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t69_41066/04_2024/8t69_41066_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t69_41066/04_2024/8t69_41066_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t69_41066/04_2024/8t69_41066_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t69_41066/04_2024/8t69_41066.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t69_41066/04_2024/8t69_41066.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t69_41066/04_2024/8t69_41066_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t69_41066/04_2024/8t69_41066_updated.pdb" } resolution = 2.89 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= 0.032 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 1950 2.51 5 N 450 2.21 5 O 495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 27": "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: 2923 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2900 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 23, 'TRANS': 362} Chain breaks: 1 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'YHL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.10, per 1000 atoms: 0.72 Number of scatterers: 2923 At special positions: 0 Unit cell: (70.741, 62.304, 64.251, 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 495 8.00 N 450 7.00 C 1950 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: 1.15 Conformation dependent library (CDL) restraints added in 541.8 milliseconds 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 0 sheets defined 85.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 20 through 48 removed outlier: 4.537A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix removed outlier: 3.504A pdb=" N LEU A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 156 removed outlier: 4.391A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.961A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 178 removed outlier: 3.734A pdb=" N PHE A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 210 removed outlier: 4.156A pdb=" N GLY A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 245 Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 250 through 270 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 292 through 314 removed outlier: 3.802A pdb=" N ASN A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET A 306 " --> pdb=" O CYS A 302 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 327 through 355 removed outlier: 4.442A pdb=" N ALA A 333 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE A 334 " --> pdb=" O GLY A 331 " (cutoff:3.500A) Proline residue: A 336 - end of helix removed outlier: 3.539A pdb=" N SER A 340 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 347 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY A 349 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA A 352 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS A 353 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET A 355 " --> pdb=" O ALA A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 373 Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 382 through 413 removed outlier: 4.421A pdb=" N ALA A 386 " --> pdb=" O GLY A 383 " (cutoff:3.500A) Proline residue: A 387 - end of helix removed outlier: 4.664A pdb=" N MET A 403 " --> pdb=" O SER A 400 " (cutoff:3.500A) Proline residue: A 404 - end of helix removed outlier: 3.666A pdb=" N LEU A 409 " --> pdb=" O MET A 406 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 412 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG A 413 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 446 removed outlier: 4.137A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 4.193A pdb=" N GLY A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 470 Proline residue: A 465 - end of helix removed outlier: 4.554A pdb=" N PHE A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N PHE A 469 " --> pdb=" O PRO A 465 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) 205 hydrogen bonds defined for protein. 516 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: 0.80 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 511 1.33 - 1.45: 707 1.45 - 1.57: 1728 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 2994 Sorted by residual: bond pdb=" C15 YHL A 901 " pdb=" C16 YHL A 901 " ideal model delta sigma weight residual 1.577 1.510 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C ILE A 375 " pdb=" N PRO A 376 " ideal model delta sigma weight residual 1.335 1.360 -0.026 1.19e-02 7.06e+03 4.73e+00 bond pdb=" C12 YHL A 901 " pdb=" O22 YHL A 901 " ideal model delta sigma weight residual 1.399 1.365 0.034 2.00e-02 2.50e+03 2.97e+00 bond pdb=" C13 YHL A 901 " pdb=" O20 YHL A 901 " ideal model delta sigma weight residual 1.399 1.365 0.034 2.00e-02 2.50e+03 2.96e+00 bond pdb=" C16 YHL A 901 " pdb=" N7 YHL A 901 " ideal model delta sigma weight residual 1.482 1.510 -0.028 2.00e-02 2.50e+03 1.90e+00 ... (remaining 2989 not shown) Histogram of bond angle deviations from ideal: 99.25 - 106.19: 107 106.19 - 113.13: 1616 113.13 - 120.07: 1089 120.07 - 127.01: 1228 127.01 - 133.95: 34 Bond angle restraints: 4074 Sorted by residual: angle pdb=" N TYR A 158 " pdb=" CA TYR A 158 " pdb=" C TYR A 158 " ideal model delta sigma weight residual 109.81 117.37 -7.56 2.21e+00 2.05e-01 1.17e+01 angle pdb=" C CYS A 374 " pdb=" N ILE A 375 " pdb=" CA ILE A 375 " ideal model delta sigma weight residual 120.33 122.97 -2.64 8.00e-01 1.56e+00 1.09e+01 angle pdb=" C ILE A 435 " pdb=" N GLY A 436 " pdb=" CA GLY A 436 " ideal model delta sigma weight residual 121.13 123.23 -2.10 7.30e-01 1.88e+00 8.28e+00 angle pdb=" C6 YHL A 901 " pdb=" N7 YHL A 901 " pdb=" C8 YHL A 901 " ideal model delta sigma weight residual 104.16 112.05 -7.89 3.00e+00 1.11e-01 6.91e+00 angle pdb=" C PHE A 245 " pdb=" N VAL A 246 " pdb=" CA VAL A 246 " ideal model delta sigma weight residual 123.16 120.46 2.70 1.06e+00 8.90e-01 6.46e+00 ... (remaining 4069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.55: 1578 12.55 - 25.10: 139 25.10 - 37.65: 32 37.65 - 50.20: 7 50.20 - 62.76: 1 Dihedral angle restraints: 1757 sinusoidal: 664 harmonic: 1093 Sorted by residual: dihedral pdb=" CA VAL A 417 " pdb=" C VAL A 417 " pdb=" N TYR A 418 " pdb=" CA TYR A 418 " ideal model delta harmonic sigma weight residual -180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA VAL A 332 " pdb=" C VAL A 332 " pdb=" N ALA A 333 " pdb=" CA ALA A 333 " ideal model delta harmonic sigma weight residual 180.00 -161.38 -18.62 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA SER A 401 " pdb=" C SER A 401 " pdb=" N MET A 402 " pdb=" CA MET A 402 " ideal model delta harmonic sigma weight residual -180.00 -163.78 -16.22 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 1754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 284 0.029 - 0.058: 120 0.058 - 0.087: 51 0.087 - 0.116: 23 0.116 - 0.145: 7 Chirality restraints: 485 Sorted by residual: chirality pdb=" CA TYR A 158 " pdb=" N TYR A 158 " pdb=" C TYR A 158 " pdb=" CB TYR A 158 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA TYR A 422 " pdb=" N TYR A 422 " pdb=" C TYR A 422 " pdb=" CB TYR A 422 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA VAL A 417 " pdb=" N VAL A 417 " pdb=" C VAL A 417 " pdb=" CB VAL A 417 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 482 not shown) Planarity restraints: 498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 436 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO A 437 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 437 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 437 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.28e+00 pdb=" N PRO A 236 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 202 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C ALA A 202 " -0.024 2.00e-02 2.50e+03 pdb=" O ALA A 202 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY A 203 " 0.008 2.00e-02 2.50e+03 ... (remaining 495 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 1075 2.88 - 3.39: 3182 3.39 - 3.89: 5038 3.89 - 4.40: 5763 4.40 - 4.90: 9900 Nonbonded interactions: 24958 Sorted by model distance: nonbonded pdb=" OD1 ASP A 411 " pdb=" OG SER A 416 " model vdw 2.381 2.440 nonbonded pdb=" OH TYR A 47 " pdb=" O SER A 179 " model vdw 2.388 2.440 nonbonded pdb=" O MET A 397 " pdb=" OG SER A 401 " model vdw 2.424 2.440 nonbonded pdb=" O TYR A 341 " pdb=" OG1 THR A 345 " model vdw 2.428 2.440 nonbonded pdb=" OH TYR A 341 " pdb=" OD2 ASP A 399 " model vdw 2.449 2.440 ... (remaining 24953 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: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.500 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.080 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:10.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 : 0.004 0.067 2994 Z= 0.241 Angle : 0.725 7.888 4074 Z= 0.371 Chirality : 0.042 0.145 485 Planarity : 0.006 0.047 498 Dihedral : 10.382 62.755 1061 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.64 % Allowed : 3.22 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.45), residues: 382 helix: 1.02 (0.31), residues: 296 sheet: None (None), residues: 0 loop : 0.11 (0.75), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.016 0.002 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.003 0.001 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.283 Fit side-chains REVERT: A 33 ASP cc_start: 0.7044 (t0) cc_final: 0.6738 (t0) REVERT: A 319 MET cc_start: 0.6211 (mtm) cc_final: 0.5653 (mmp) REVERT: A 403 MET cc_start: 0.8573 (mmm) cc_final: 0.8127 (mmm) outliers start: 2 outliers final: 0 residues processed: 59 average time/residue: 0.8373 time to fit residues: 51.3198 Evaluate side-chains 43 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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: 1.9990 chunk 28 optimal weight: 0.0770 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 0.1980 chunk 10 optimal weight: 0.5980 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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: 0.7893 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2994 Z= 0.198 Angle : 0.615 6.510 4074 Z= 0.314 Chirality : 0.042 0.135 485 Planarity : 0.007 0.046 498 Dihedral : 5.012 22.526 418 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.25 % Allowed : 8.04 % Favored : 89.71 % 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: 1.05 (0.45), residues: 382 helix: 0.91 (0.31), residues: 297 sheet: None (None), residues: 0 loop : 0.31 (0.77), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.001 0.000 HIS A 353 PHE 0.016 0.001 PHE A 176 TYR 0.011 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.335 Fit side-chains REVERT: A 33 ASP cc_start: 0.6943 (t0) cc_final: 0.6676 (t0) REVERT: A 169 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.6461 (ttm) REVERT: A 319 MET cc_start: 0.6350 (mtm) cc_final: 0.5841 (mmp) outliers start: 7 outliers final: 2 residues processed: 48 average time/residue: 1.0399 time to fit residues: 51.6834 Evaluate side-chains 44 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.0020 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.0970 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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: 0.7894 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2994 Z= 0.189 Angle : 0.577 6.660 4074 Z= 0.287 Chirality : 0.041 0.125 485 Planarity : 0.006 0.046 498 Dihedral : 4.737 20.808 418 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.25 % Allowed : 10.61 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.45), residues: 382 helix: 1.06 (0.31), residues: 297 sheet: None (None), residues: 0 loop : 0.02 (0.76), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 358 HIS 0.001 0.001 HIS A 353 PHE 0.013 0.001 PHE A 27 TYR 0.015 0.001 TYR A 422 ARG 0.002 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.309 Fit side-chains REVERT: A 33 ASP cc_start: 0.6951 (t0) cc_final: 0.6656 (t0) REVERT: A 169 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7707 (tpp) REVERT: A 319 MET cc_start: 0.6500 (mtm) cc_final: 0.6034 (mmp) outliers start: 7 outliers final: 3 residues processed: 48 average time/residue: 1.0484 time to fit residues: 52.0227 Evaluate side-chains 45 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 273 SER 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: 4.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2994 Z= 0.328 Angle : 0.669 6.827 4074 Z= 0.332 Chirality : 0.045 0.153 485 Planarity : 0.007 0.051 498 Dihedral : 4.977 21.489 418 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.22 % Allowed : 8.36 % Favored : 88.42 % 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: 0.63 (0.45), residues: 382 helix: 0.74 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -0.47 (0.75), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 451 HIS 0.001 0.001 HIS A 353 PHE 0.016 0.002 PHE A 238 TYR 0.018 0.002 TYR A 422 ARG 0.003 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.327 Fit side-chains REVERT: A 33 ASP cc_start: 0.7203 (t0) cc_final: 0.6858 (t0) REVERT: A 169 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7724 (tpp) REVERT: A 276 GLN cc_start: 0.6479 (OUTLIER) cc_final: 0.5950 (mt0) REVERT: A 319 MET cc_start: 0.6698 (mtm) cc_final: 0.6187 (mmp) REVERT: A 403 MET cc_start: 0.8700 (mmm) cc_final: 0.8308 (mmm) outliers start: 10 outliers final: 5 residues processed: 44 average time/residue: 1.0291 time to fit residues: 46.9119 Evaluate side-chains 45 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 332 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.0270 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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: 0.7928 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2994 Z= 0.211 Angle : 0.573 6.660 4074 Z= 0.288 Chirality : 0.041 0.132 485 Planarity : 0.006 0.048 498 Dihedral : 4.739 20.294 418 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.57 % Allowed : 9.32 % Favored : 88.10 % 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 (0.46), residues: 382 helix: 0.99 (0.32), residues: 302 sheet: None (None), residues: 0 loop : -0.32 (0.76), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 358 HIS 0.001 0.000 HIS A 353 PHE 0.010 0.001 PHE A 348 TYR 0.016 0.001 TYR A 422 ARG 0.002 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.390 Fit side-chains REVERT: A 33 ASP cc_start: 0.7070 (t0) cc_final: 0.6741 (t0) REVERT: A 169 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7684 (tpp) REVERT: A 273 SER cc_start: 0.7821 (OUTLIER) cc_final: 0.7320 (p) REVERT: A 276 GLN cc_start: 0.6375 (OUTLIER) cc_final: 0.5876 (mt0) REVERT: A 319 MET cc_start: 0.6668 (mtm) cc_final: 0.6222 (mmp) outliers start: 8 outliers final: 4 residues processed: 44 average time/residue: 1.0003 time to fit residues: 45.5635 Evaluate side-chains 44 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 401 SER 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: 1.9990 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7961 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2994 Z= 0.260 Angle : 0.612 6.775 4074 Z= 0.304 Chirality : 0.042 0.142 485 Planarity : 0.006 0.048 498 Dihedral : 4.788 20.763 418 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.89 % Allowed : 9.00 % Favored : 88.10 % 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: 0.86 (0.45), residues: 382 helix: 0.91 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -0.45 (0.77), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 358 HIS 0.001 0.000 HIS A 353 PHE 0.013 0.002 PHE A 348 TYR 0.018 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.328 Fit side-chains REVERT: A 33 ASP cc_start: 0.7125 (t0) cc_final: 0.6773 (t0) REVERT: A 169 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7048 (tpt) REVERT: A 276 GLN cc_start: 0.6457 (OUTLIER) cc_final: 0.5950 (mt0) REVERT: A 319 MET cc_start: 0.6765 (mtm) cc_final: 0.6307 (mmp) outliers start: 9 outliers final: 5 residues processed: 45 average time/residue: 1.0058 time to fit residues: 46.9202 Evaluate side-chains 44 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 401 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2994 Z= 0.249 Angle : 0.598 6.770 4074 Z= 0.298 Chirality : 0.042 0.139 485 Planarity : 0.006 0.047 498 Dihedral : 4.734 20.266 418 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.22 % Allowed : 9.65 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.46), residues: 382 helix: 0.95 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -0.53 (0.77), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 358 HIS 0.001 0.000 HIS A 353 PHE 0.012 0.001 PHE A 348 TYR 0.017 0.002 TYR A 422 ARG 0.001 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 0.337 Fit side-chains REVERT: A 33 ASP cc_start: 0.7150 (t0) cc_final: 0.6780 (t0) REVERT: A 169 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7665 (tpp) REVERT: A 276 GLN cc_start: 0.6435 (OUTLIER) cc_final: 0.5929 (mt0) REVERT: A 319 MET cc_start: 0.6919 (mtm) cc_final: 0.6481 (mmp) outliers start: 10 outliers final: 7 residues processed: 44 average time/residue: 1.0161 time to fit residues: 46.3467 Evaluate side-chains 47 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 401 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.0020 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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: 0.7954 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2994 Z= 0.237 Angle : 0.587 6.770 4074 Z= 0.293 Chirality : 0.042 0.137 485 Planarity : 0.006 0.047 498 Dihedral : 4.695 20.354 418 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.89 % Allowed : 9.65 % Favored : 87.46 % 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: 0.92 (0.46), residues: 382 helix: 0.99 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -0.57 (0.77), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 358 HIS 0.001 0.000 HIS A 353 PHE 0.012 0.001 PHE A 348 TYR 0.018 0.001 TYR A 422 ARG 0.003 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.337 Fit side-chains REVERT: A 33 ASP cc_start: 0.7126 (t0) cc_final: 0.6776 (t0) REVERT: A 169 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7080 (tpt) REVERT: A 273 SER cc_start: 0.7858 (OUTLIER) cc_final: 0.7352 (p) REVERT: A 276 GLN cc_start: 0.6430 (OUTLIER) cc_final: 0.5926 (mt0) REVERT: A 319 MET cc_start: 0.6956 (mtm) cc_final: 0.6528 (mmp) outliers start: 9 outliers final: 5 residues processed: 43 average time/residue: 1.0518 time to fit residues: 46.7994 Evaluate side-chains 45 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 401 SER 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: 0.5980 chunk 34 optimal weight: 0.0570 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.0010 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 overall best weight: 0.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2994 Z= 0.170 Angle : 0.540 6.636 4074 Z= 0.272 Chirality : 0.040 0.129 485 Planarity : 0.006 0.047 498 Dihedral : 4.525 19.278 418 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.22 % Allowed : 9.97 % Favored : 86.82 % 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: 1.11 (0.46), residues: 382 helix: 1.10 (0.32), residues: 307 sheet: None (None), residues: 0 loop : -0.49 (0.80), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 358 HIS 0.000 0.000 HIS A 353 PHE 0.009 0.001 PHE A 238 TYR 0.016 0.001 TYR A 422 ARG 0.002 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.365 Fit side-chains REVERT: A 33 ASP cc_start: 0.7007 (t0) cc_final: 0.6661 (t0) REVERT: A 35 MET cc_start: 0.9105 (ttm) cc_final: 0.8842 (mtp) REVERT: A 169 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7021 (tpt) REVERT: A 273 SER cc_start: 0.7763 (OUTLIER) cc_final: 0.7264 (p) REVERT: A 276 GLN cc_start: 0.6359 (OUTLIER) cc_final: 0.5872 (mt0) REVERT: A 319 MET cc_start: 0.6956 (mtm) cc_final: 0.6513 (mmp) outliers start: 10 outliers final: 6 residues processed: 46 average time/residue: 0.9973 time to fit residues: 47.5897 Evaluate side-chains 45 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 401 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7929 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2994 Z= 0.216 Angle : 0.574 6.756 4074 Z= 0.287 Chirality : 0.041 0.132 485 Planarity : 0.006 0.046 498 Dihedral : 4.570 20.058 418 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.89 % Allowed : 10.93 % Favored : 86.17 % 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: 1.01 (0.46), residues: 382 helix: 1.01 (0.31), residues: 308 sheet: None (None), residues: 0 loop : -0.47 (0.79), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 358 HIS 0.000 0.000 HIS A 353 PHE 0.011 0.001 PHE A 348 TYR 0.019 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.317 Fit side-chains REVERT: A 33 ASP cc_start: 0.7054 (t0) cc_final: 0.6704 (t0) REVERT: A 35 MET cc_start: 0.9104 (ttm) cc_final: 0.8849 (mtp) REVERT: A 169 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7045 (tpt) REVERT: A 273 SER cc_start: 0.7812 (OUTLIER) cc_final: 0.7311 (p) REVERT: A 276 GLN cc_start: 0.6408 (OUTLIER) cc_final: 0.5912 (mt0) REVERT: A 319 MET cc_start: 0.7015 (mtm) cc_final: 0.6550 (mmp) outliers start: 9 outliers final: 6 residues processed: 45 average time/residue: 0.9910 time to fit residues: 46.2201 Evaluate side-chains 47 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 401 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.0470 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.161177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.142367 restraints weight = 3113.874| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.61 r_work: 0.3560 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2994 Z= 0.234 Angle : 0.587 6.766 4074 Z= 0.294 Chirality : 0.042 0.141 485 Planarity : 0.006 0.045 498 Dihedral : 4.613 20.220 418 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.89 % Allowed : 11.90 % Favored : 85.21 % 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: 1.06 (0.46), residues: 382 helix: 1.06 (0.32), residues: 303 sheet: None (None), residues: 0 loop : -0.42 (0.78), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 358 HIS 0.000 0.000 HIS A 353 PHE 0.011 0.001 PHE A 348 TYR 0.019 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1620.96 seconds wall clock time: 29 minutes 25.36 seconds (1765.36 seconds total)