Starting phenix.real_space_refine on Fri Apr 5 16:39:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdy_40354/04_2024/8sdy_40354_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdy_40354/04_2024/8sdy_40354.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdy_40354/04_2024/8sdy_40354_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdy_40354/04_2024/8sdy_40354_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdy_40354/04_2024/8sdy_40354_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdy_40354/04_2024/8sdy_40354.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdy_40354/04_2024/8sdy_40354.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdy_40354/04_2024/8sdy_40354_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdy_40354/04_2024/8sdy_40354_updated.pdb" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2528 2.51 5 N 653 2.21 5 O 683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 157": "OD1" <-> "OD2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A PHE 442": "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: 3894 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3840 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3831 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 25, 'TRANS': 468} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 494, 3831 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 25, 'TRANS': 468} Chain breaks: 3 bond proxies already assigned to first conformer: 3912 Chain: "A" Number of atoms: 54 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 13, 26 Unusual residues: {'ZWD': 1} Classifications: {'undetermined': 1, 'water': 12} Link IDs: {None: 12} Conformer: "B" Number of residues, atoms: 13, 26 Unusual residues: {'ZWD': 1} Classifications: {'undetermined': 1, 'water': 12} Link IDs: {None: 12} Conformer: "C" Number of residues, atoms: 13, 26 Unusual residues: {'ZWD': 1} Classifications: {'undetermined': 1, 'water': 12} Link IDs: {None: 12} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALYS A 382 " occ=0.52 ... (16 atoms not shown) pdb=" NZ BLYS A 382 " occ=0.48 residue: pdb=" C01AZWD A 601 " occ=0.85 ... (40 atoms not shown) pdb=" O13CZWD A 601 " occ=0.14 Time building chain proxies: 4.48, per 1000 atoms: 1.15 Number of scatterers: 3894 At special positions: 0 Unit cell: (85.49, 68.89, 94.62, 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 30 16.00 O 683 8.00 N 653 7.00 C 2528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " distance=2.02 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: 1.56 Conformation dependent library (CDL) restraints added in 1.8 seconds 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 918 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 1 sheets defined 73.9% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 Processing helix chain 'A' and resid 15 through 35 Proline residue: A 27 - end of helix removed outlier: 4.331A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 41 removed outlier: 3.774A pdb=" N THR A 41 " --> pdb=" O GLN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 132 through 159 removed outlier: 3.637A pdb=" N GLN A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG A 158 " --> pdb=" O TYR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 180 Processing helix chain 'A' and resid 185 through 212 removed outlier: 3.844A pdb=" N MET A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 243 removed outlier: 4.052A pdb=" N ARG A 219 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ALA A 220 " --> pdb=" O HIS A 217 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 237 " --> pdb=" O GLN A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 267 Proline residue: A 257 - end of helix removed outlier: 3.966A pdb=" N ILE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TRP A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N PHE A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.786A pdb=" N LYS A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.703A pdb=" N LEU A 330 " --> pdb=" O MET A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 357 removed outlier: 3.861A pdb=" N LEU A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 363 removed outlier: 4.128A pdb=" N PHE A 363 " --> pdb=" O LEU A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 367 through 391 removed outlier: 3.950A pdb=" N ASP A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 394 through 414 Processing helix chain 'A' and resid 420 through 448 Processing helix chain 'A' and resid 454 through 480 Proline residue: A 473 - end of helix removed outlier: 4.116A pdb=" N THR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ALA A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 503 Proline residue: A 494 - end of helix removed outlier: 3.813A pdb=" N ALA A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU A 503 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 523 Processing sheet with id= A, first strand: chain 'A' and resid 47 through 49 239 hydrogen bonds defined for protein. 643 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.04 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 586 1.31 - 1.44: 1105 1.44 - 1.56: 2236 1.56 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 3974 Sorted by residual: bond pdb=" N ALA A 2 " pdb=" CA ALA A 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" CB PHE A 442 " pdb=" CG PHE A 442 " ideal model delta sigma weight residual 1.502 1.530 -0.028 2.30e-02 1.89e+03 1.53e+00 bond pdb=" CB GLN A 289 " pdb=" CG GLN A 289 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.55e-01 bond pdb=" CA TYR A 264 " pdb=" CB TYR A 264 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.78e-02 3.16e+03 6.25e-01 bond pdb=" C ALA A 435 " pdb=" O ALA A 435 " ideal model delta sigma weight residual 1.237 1.246 -0.009 1.17e-02 7.31e+03 5.85e-01 ... (remaining 3969 not shown) Histogram of bond angle deviations from ideal: 100.77 - 107.42: 151 107.42 - 114.07: 2225 114.07 - 120.72: 1834 120.72 - 127.37: 1142 127.37 - 134.02: 50 Bond angle restraints: 5402 Sorted by residual: angle pdb=" CA GLN A 289 " pdb=" CB GLN A 289 " pdb=" CG GLN A 289 " ideal model delta sigma weight residual 114.10 120.60 -6.50 2.00e+00 2.50e-01 1.06e+01 angle pdb=" CA TYR A 264 " pdb=" CB TYR A 264 " pdb=" CG TYR A 264 " ideal model delta sigma weight residual 113.90 119.00 -5.10 1.80e+00 3.09e-01 8.02e+00 angle pdb=" CG ARG A 290 " pdb=" CD ARG A 290 " pdb=" NE ARG A 290 " ideal model delta sigma weight residual 112.00 117.66 -5.66 2.20e+00 2.07e-01 6.62e+00 angle pdb=" N VAL A 256 " pdb=" CA VAL A 256 " pdb=" C VAL A 256 " ideal model delta sigma weight residual 108.88 113.60 -4.72 2.16e+00 2.14e-01 4.78e+00 angle pdb=" CA CYS A 105 " pdb=" C CYS A 105 " pdb=" N ILE A 106 " ideal model delta sigma weight residual 114.76 117.20 -2.44 1.14e+00 7.69e-01 4.59e+00 ... (remaining 5397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 1994 17.59 - 35.18: 254 35.18 - 52.77: 75 52.77 - 70.36: 10 70.36 - 87.95: 4 Dihedral angle restraints: 2337 sinusoidal: 908 harmonic: 1429 Sorted by residual: dihedral pdb=" CG ARG A 290 " pdb=" CD ARG A 290 " pdb=" NE ARG A 290 " pdb=" CZ ARG A 290 " ideal model delta sinusoidal sigma weight residual 90.00 41.14 48.86 2 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CG ARG A 280 " pdb=" CD ARG A 280 " pdb=" NE ARG A 280 " pdb=" CZ ARG A 280 " ideal model delta sinusoidal sigma weight residual 180.00 136.55 43.45 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CG ARG A 80 " pdb=" CD ARG A 80 " pdb=" NE ARG A 80 " pdb=" CZ ARG A 80 " ideal model delta sinusoidal sigma weight residual 90.00 133.22 -43.22 2 1.50e+01 4.44e-03 1.00e+01 ... (remaining 2334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 390 0.027 - 0.055: 149 0.055 - 0.082: 58 0.082 - 0.110: 20 0.110 - 0.137: 8 Chirality restraints: 625 Sorted by residual: chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE A 269 " pdb=" N ILE A 269 " pdb=" C ILE A 269 " pdb=" CB ILE A 269 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE A 415 " pdb=" N ILE A 415 " pdb=" C ILE A 415 " pdb=" CB ILE A 415 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 622 not shown) Planarity restraints: 673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 290 " -0.202 9.50e-02 1.11e+02 9.10e-02 5.88e+00 pdb=" NE ARG A 290 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 290 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 290 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 290 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 395 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.89e+00 pdb=" N PRO A 396 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 332 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO A 333 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 333 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 333 " -0.015 5.00e-02 4.00e+02 ... (remaining 670 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 40 2.59 - 3.17: 3478 3.17 - 3.75: 6390 3.75 - 4.32: 8892 4.32 - 4.90: 14729 Nonbonded interactions: 33529 Sorted by model distance: nonbonded pdb=" OH TYR A 444 " pdb=" O PRO A 505 " model vdw 2.018 2.440 nonbonded pdb=" OG SER A 33 " pdb=" O HOH A 701 " model vdw 2.066 2.440 nonbonded pdb=" OD1 ASN A 168 " pdb=" OG SER A 201 " model vdw 2.201 2.440 nonbonded pdb=" NH2 ARG A 80 " pdb=" OE2 GLU A 103 " model vdw 2.222 2.520 nonbonded pdb=" OG1 THR A 172 " pdb=" OG SER A 198 " model vdw 2.226 2.440 ... (remaining 33524 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=0.01 max=1.00 mean=0.99 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: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.060 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.350 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 : 0.003 0.035 3974 Z= 0.223 Angle : 0.595 6.497 5402 Z= 0.304 Chirality : 0.037 0.137 625 Planarity : 0.005 0.091 673 Dihedral : 16.732 87.947 1413 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.72 % Allowed : 23.50 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.38), residues: 489 helix: 1.62 (0.27), residues: 374 sheet: -2.13 (1.49), residues: 10 loop : 1.03 (0.65), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.003 0.001 HIS A 217 PHE 0.013 0.001 PHE A 442 TYR 0.016 0.001 TYR A 264 ARG 0.016 0.001 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.452 Fit side-chains REVERT: A 290 ARG cc_start: 0.6347 (mtp85) cc_final: 0.6129 (mmm-85) REVERT: A 389 ILE cc_start: 0.7839 (mt) cc_final: 0.7617 (mp) REVERT: A 437 SER cc_start: 0.8553 (t) cc_final: 0.8204 (p) REVERT: A 460 MET cc_start: 0.7089 (mmm) cc_final: 0.6785 (mmm) outliers start: 3 outliers final: 3 residues processed: 52 average time/residue: 1.1224 time to fit residues: 60.7139 Evaluate side-chains 52 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 462 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.0658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3974 Z= 0.230 Angle : 0.551 6.234 5402 Z= 0.280 Chirality : 0.039 0.156 625 Planarity : 0.005 0.035 673 Dihedral : 5.613 54.403 551 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.40 % Allowed : 21.58 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.39), residues: 489 helix: 1.62 (0.27), residues: 373 sheet: -1.70 (1.38), residues: 10 loop : 0.85 (0.65), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 346 HIS 0.003 0.001 HIS A 48 PHE 0.013 0.001 PHE A 442 TYR 0.018 0.001 TYR A 264 ARG 0.007 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.434 Fit side-chains REVERT: A 289 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7623 (tp-100) REVERT: A 437 SER cc_start: 0.8589 (t) cc_final: 0.8266 (p) REVERT: A 460 MET cc_start: 0.7130 (mmm) cc_final: 0.6806 (mmm) outliers start: 10 outliers final: 4 residues processed: 52 average time/residue: 1.0771 time to fit residues: 58.3751 Evaluate side-chains 51 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3974 Z= 0.184 Angle : 0.522 7.017 5402 Z= 0.264 Chirality : 0.037 0.153 625 Planarity : 0.004 0.034 673 Dihedral : 5.378 53.462 549 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.16 % Allowed : 22.30 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.39), residues: 489 helix: 1.72 (0.27), residues: 367 sheet: -1.53 (1.46), residues: 10 loop : 0.93 (0.65), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 213 HIS 0.002 0.001 HIS A 48 PHE 0.012 0.001 PHE A 351 TYR 0.016 0.001 TYR A 264 ARG 0.006 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.371 Fit side-chains REVERT: A 225 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.5874 (pp) REVERT: A 313 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6758 (mm) REVERT: A 437 SER cc_start: 0.8602 (t) cc_final: 0.8307 (p) REVERT: A 460 MET cc_start: 0.7101 (mmt) cc_final: 0.6772 (mmm) outliers start: 9 outliers final: 2 residues processed: 52 average time/residue: 1.0192 time to fit residues: 55.3496 Evaluate side-chains 53 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 21 optimal weight: 0.0870 chunk 29 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3974 Z= 0.161 Angle : 0.497 7.003 5402 Z= 0.249 Chirality : 0.037 0.138 625 Planarity : 0.004 0.038 673 Dihedral : 5.158 51.637 549 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.88 % Allowed : 20.62 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.39), residues: 489 helix: 1.77 (0.28), residues: 367 sheet: -1.37 (1.50), residues: 10 loop : 1.00 (0.65), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 213 HIS 0.002 0.000 HIS A 217 PHE 0.013 0.001 PHE A 351 TYR 0.015 0.001 TYR A 264 ARG 0.008 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.432 Fit side-chains REVERT: A 225 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.5814 (pp) REVERT: A 313 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6741 (mm) REVERT: A 389 ILE cc_start: 0.7830 (mt) cc_final: 0.7602 (mp) REVERT: A 394 ARG cc_start: 0.6255 (mpt180) cc_final: 0.5441 (mpt180) REVERT: A 437 SER cc_start: 0.8594 (t) cc_final: 0.8310 (p) REVERT: A 460 MET cc_start: 0.7120 (mmt) cc_final: 0.6812 (mmm) outliers start: 12 outliers final: 3 residues processed: 57 average time/residue: 1.0816 time to fit residues: 64.1888 Evaluate side-chains 51 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 27 optimal weight: 0.0010 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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: 0.7940 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3974 Z= 0.158 Angle : 0.497 6.985 5402 Z= 0.246 Chirality : 0.037 0.128 625 Planarity : 0.004 0.028 673 Dihedral : 5.010 50.189 549 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.16 % Allowed : 21.10 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.39), residues: 489 helix: 1.76 (0.28), residues: 367 sheet: -1.39 (1.47), residues: 10 loop : 0.99 (0.64), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.002 0.000 HIS A 217 PHE 0.012 0.001 PHE A 351 TYR 0.016 0.001 TYR A 264 ARG 0.006 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.472 Fit side-chains REVERT: A 225 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.5771 (pp) REVERT: A 313 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6748 (mm) REVERT: A 437 SER cc_start: 0.8597 (t) cc_final: 0.8312 (p) REVERT: A 458 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8025 (mp) REVERT: A 460 MET cc_start: 0.7115 (mmt) cc_final: 0.6807 (mmm) outliers start: 9 outliers final: 4 residues processed: 53 average time/residue: 1.0736 time to fit residues: 59.2831 Evaluate side-chains 53 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 458 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3974 Z= 0.176 Angle : 0.505 6.459 5402 Z= 0.252 Chirality : 0.037 0.138 625 Planarity : 0.004 0.031 673 Dihedral : 4.976 49.215 549 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.40 % Allowed : 21.58 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.39), residues: 489 helix: 1.70 (0.27), residues: 367 sheet: -1.46 (1.46), residues: 10 loop : 0.95 (0.63), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.002 0.001 HIS A 48 PHE 0.011 0.001 PHE A 351 TYR 0.017 0.001 TYR A 264 ARG 0.008 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.463 Fit side-chains REVERT: A 225 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.5820 (pp) REVERT: A 313 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6780 (mm) REVERT: A 389 ILE cc_start: 0.7864 (mt) cc_final: 0.7570 (mp) REVERT: A 392 MET cc_start: 0.5113 (OUTLIER) cc_final: 0.4740 (mtm) REVERT: A 394 ARG cc_start: 0.6252 (mpt180) cc_final: 0.5695 (mtm-85) REVERT: A 437 SER cc_start: 0.8608 (t) cc_final: 0.8302 (p) REVERT: A 460 MET cc_start: 0.7139 (mmt) cc_final: 0.6838 (mmm) outliers start: 10 outliers final: 4 residues processed: 56 average time/residue: 1.0565 time to fit residues: 61.6151 Evaluate side-chains 59 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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: 0.7968 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3974 Z= 0.184 Angle : 0.515 6.473 5402 Z= 0.258 Chirality : 0.038 0.180 625 Planarity : 0.004 0.034 673 Dihedral : 4.954 48.487 549 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.64 % Allowed : 21.34 % Favored : 76.02 % 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: 1.95 (0.39), residues: 489 helix: 1.58 (0.27), residues: 373 sheet: -1.46 (1.48), residues: 10 loop : 0.84 (0.64), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.002 0.001 HIS A 48 PHE 0.011 0.001 PHE A 351 TYR 0.018 0.001 TYR A 264 ARG 0.007 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 50 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 225 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.5817 (pp) REVERT: A 313 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6785 (mm) REVERT: A 392 MET cc_start: 0.5114 (OUTLIER) cc_final: 0.4750 (mtm) REVERT: A 437 SER cc_start: 0.8610 (t) cc_final: 0.8302 (p) REVERT: A 460 MET cc_start: 0.7152 (mmt) cc_final: 0.6835 (mmm) outliers start: 11 outliers final: 6 residues processed: 56 average time/residue: 1.1806 time to fit residues: 68.6515 Evaluate side-chains 58 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 444 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 26 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.7957 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 3974 Z= 0.191 Angle : 0.522 7.467 5402 Z= 0.264 Chirality : 0.037 0.165 625 Planarity : 0.004 0.034 673 Dihedral : 4.905 47.809 549 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.16 % Allowed : 22.30 % Favored : 75.54 % 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: 1.98 (0.39), residues: 489 helix: 1.59 (0.27), residues: 367 sheet: -1.44 (1.50), residues: 10 loop : 0.94 (0.63), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.002 0.001 HIS A 48 PHE 0.011 0.001 PHE A 351 TYR 0.017 0.001 TYR A 264 ARG 0.008 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 225 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.5793 (pp) REVERT: A 313 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6727 (mm) REVERT: A 437 SER cc_start: 0.8606 (t) cc_final: 0.8310 (p) REVERT: A 458 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8033 (mp) REVERT: A 460 MET cc_start: 0.7138 (mmt) cc_final: 0.6828 (mmm) outliers start: 9 outliers final: 5 residues processed: 55 average time/residue: 1.0898 time to fit residues: 62.3568 Evaluate side-chains 58 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 458 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 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: 0.7948 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3974 Z= 0.182 Angle : 0.515 7.047 5402 Z= 0.259 Chirality : 0.037 0.163 625 Planarity : 0.004 0.033 673 Dihedral : 4.823 47.116 549 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.16 % Allowed : 22.78 % Favored : 75.06 % 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: 1.99 (0.39), residues: 489 helix: 1.59 (0.27), residues: 367 sheet: -1.41 (1.51), residues: 10 loop : 0.96 (0.63), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.002 0.001 HIS A 48 PHE 0.012 0.001 PHE A 351 TYR 0.017 0.001 TYR A 264 ARG 0.008 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 225 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.5755 (pp) REVERT: A 290 ARG cc_start: 0.6594 (mmm-85) cc_final: 0.6384 (mtp85) REVERT: A 313 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6693 (mm) REVERT: A 437 SER cc_start: 0.8605 (t) cc_final: 0.8313 (p) REVERT: A 458 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8029 (mp) REVERT: A 460 MET cc_start: 0.7131 (mmt) cc_final: 0.6823 (mmm) outliers start: 9 outliers final: 6 residues processed: 54 average time/residue: 1.1468 time to fit residues: 64.3166 Evaluate side-chains 58 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 458 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7907 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 3974 Z= 0.166 Angle : 0.505 7.045 5402 Z= 0.253 Chirality : 0.036 0.157 625 Planarity : 0.004 0.035 673 Dihedral : 4.623 45.687 549 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.16 % Allowed : 22.78 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.39), residues: 489 helix: 1.64 (0.28), residues: 370 sheet: -1.35 (1.53), residues: 10 loop : 1.21 (0.65), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.001 0.000 HIS A 48 PHE 0.012 0.001 PHE A 351 TYR 0.016 0.001 TYR A 264 ARG 0.007 0.000 ARG A 290 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.434 Fit side-chains REVERT: A 313 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6640 (mm) REVERT: A 437 SER cc_start: 0.8612 (t) cc_final: 0.8336 (p) REVERT: A 458 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7951 (mp) REVERT: A 460 MET cc_start: 0.7092 (mmt) cc_final: 0.6797 (mmm) outliers start: 9 outliers final: 4 residues processed: 55 average time/residue: 1.0338 time to fit residues: 59.2664 Evaluate side-chains 55 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 458 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 7.9990 chunk 34 optimal weight: 0.1980 chunk 2 optimal weight: 0.0570 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 26 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 = 0.4183 r_free = 0.4183 target = 0.187454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.144638 restraints weight = 12165.153| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.74 r_work: 0.3612 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 3974 Z= 0.170 Angle : 0.519 6.911 5402 Z= 0.259 Chirality : 0.037 0.158 625 Planarity : 0.004 0.036 673 Dihedral : 4.538 45.658 549 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.44 % Allowed : 23.74 % Favored : 74.82 % 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: 2.13 (0.39), residues: 489 helix: 1.62 (0.27), residues: 370 sheet: -1.32 (1.55), residues: 10 loop : 1.28 (0.65), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.002 0.000 HIS A 217 PHE 0.012 0.001 PHE A 351 TYR 0.016 0.001 TYR A 264 ARG 0.007 0.000 ARG A 290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1792.48 seconds wall clock time: 33 minutes 8.62 seconds (1988.62 seconds total)