Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 18:06:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/07_2023/7xq1_33388_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/07_2023/7xq1_33388.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/07_2023/7xq1_33388_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/07_2023/7xq1_33388_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/07_2023/7xq1_33388_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/07_2023/7xq1_33388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/07_2023/7xq1_33388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/07_2023/7xq1_33388_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/07_2023/7xq1_33388_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 14 5.16 5 C 2178 2.51 5 N 548 2.21 5 O 558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 3302 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3302 Unusual residues: {'GJF': 2} Classifications: {'peptide': 400, 'undetermined': 2} Link IDs: {'PTRANS': 14, 'TRANS': 385, None: 2} Not linked: pdbres="ASP A 453 " pdbres="GJF A 601 " Not linked: pdbres="GJF A 601 " pdbres="GJF A 602 " Chain breaks: 1 Time building chain proxies: 2.00, per 1000 atoms: 0.61 Number of scatterers: 3302 At special positions: 0 Unit cell: (79, 77, 64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 4 15.00 O 558 8.00 N 548 7.00 C 2178 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: 1.29 Conformation dependent library (CDL) restraints added in 424.7 milliseconds 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 0 sheets defined 72.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 24 through 27 No H-bonds generated for 'chain 'A' and resid 24 through 27' Processing helix chain 'A' and resid 29 through 40 removed outlier: 3.604A pdb=" N PHE A 34 " --> pdb=" O CYS A 30 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 52 No H-bonds generated for 'chain 'A' and resid 49 through 52' Processing helix chain 'A' and resid 61 through 64 No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 69 through 78 removed outlier: 3.552A pdb=" N TYR A 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER A 75 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR A 76 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 removed outlier: 3.868A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 112 removed outlier: 3.601A pdb=" N LEU A 111 " --> pdb=" O TRP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 removed outlier: 3.713A pdb=" N MET A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 removed outlier: 4.127A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 175 removed outlier: 3.521A pdb=" N LEU A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 201 removed outlier: 3.811A pdb=" N VAL A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 removed outlier: 3.683A pdb=" N GLY A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 285 removed outlier: 3.615A pdb=" N LEU A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 295 Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.565A pdb=" N ALA A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 335 through 355 removed outlier: 4.051A pdb=" N ALA A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 363 through 387 removed outlier: 3.764A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 393 through 417 removed outlier: 3.611A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 451 removed outlier: 3.765A pdb=" N GLN A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) 166 hydrogen bonds defined for protein. 486 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: 0.88 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 1050 1.37 - 1.53: 2213 1.53 - 1.69: 120 1.69 - 1.85: 17 1.85 - 2.01: 3 Bond restraints: 3403 Sorted by residual: bond pdb=" P2 GJF A 601 " pdb=" S2 GJF A 601 " ideal model delta sigma weight residual 2.121 1.766 0.355 2.00e-02 2.50e+03 3.14e+02 bond pdb=" P1 GJF A 601 " pdb=" S1 GJF A 601 " ideal model delta sigma weight residual 2.126 1.852 0.274 2.00e-02 2.50e+03 1.88e+02 bond pdb=" P2 GJF A 602 " pdb=" S2 GJF A 602 " ideal model delta sigma weight residual 2.121 1.930 0.191 2.00e-02 2.50e+03 9.13e+01 bond pdb=" C3 GJF A 601 " pdb=" N8 GJF A 601 " ideal model delta sigma weight residual 1.456 1.325 0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" C3 GJF A 602 " pdb=" N8 GJF A 602 " ideal model delta sigma weight residual 1.456 1.330 0.126 2.00e-02 2.50e+03 3.96e+01 ... (remaining 3398 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.07: 113 107.07 - 113.80: 1901 113.80 - 120.53: 1486 120.53 - 127.26: 1113 127.26 - 133.99: 45 Bond angle restraints: 4658 Sorted by residual: angle pdb=" C11 GJF A 602 " pdb=" C14 GJF A 602 " pdb=" N7 GJF A 602 " ideal model delta sigma weight residual 142.76 116.20 26.56 3.00e+00 1.11e-01 7.84e+01 angle pdb=" C11 GJF A 601 " pdb=" C14 GJF A 601 " pdb=" N7 GJF A 601 " ideal model delta sigma weight residual 142.76 116.21 26.55 3.00e+00 1.11e-01 7.83e+01 angle pdb=" N6 GJF A 601 " pdb=" C14 GJF A 601 " pdb=" N7 GJF A 601 " ideal model delta sigma weight residual 96.68 121.96 -25.28 3.00e+00 1.11e-01 7.10e+01 angle pdb=" N6 GJF A 602 " pdb=" C14 GJF A 602 " pdb=" N7 GJF A 602 " ideal model delta sigma weight residual 96.68 121.72 -25.04 3.00e+00 1.11e-01 6.97e+01 angle pdb=" C19 GJF A 601 " pdb=" N10 GJF A 601 " pdb=" C4 GJF A 601 " ideal model delta sigma weight residual 107.62 126.81 -19.19 3.00e+00 1.11e-01 4.09e+01 ... (remaining 4653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 1768 17.60 - 35.20: 96 35.20 - 52.79: 34 52.79 - 70.39: 7 70.39 - 87.99: 3 Dihedral angle restraints: 1908 sinusoidal: 729 harmonic: 1179 Sorted by residual: dihedral pdb=" C VAL A 327 " pdb=" N VAL A 327 " pdb=" CA VAL A 327 " pdb=" CB VAL A 327 " ideal model delta harmonic sigma weight residual -122.00 -133.07 11.07 0 2.50e+00 1.60e-01 1.96e+01 dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA VAL A 418 " pdb=" C VAL A 418 " pdb=" N SER A 419 " pdb=" CA SER A 419 " ideal model delta harmonic sigma weight residual -180.00 -163.75 -16.25 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 1905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 473 0.074 - 0.147: 49 0.147 - 0.220: 14 0.220 - 0.294: 4 0.294 - 0.367: 4 Chirality restraints: 544 Sorted by residual: chirality pdb=" P1 GJF A 601 " pdb=" O3 GJF A 601 " pdb=" O4 GJF A 601 " pdb=" S1 GJF A 601 " both_signs ideal model delta sigma weight residual True 3.83 -3.46 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" P2 GJF A 601 " pdb=" O5 GJF A 601 " pdb=" O6 GJF A 601 " pdb=" O9 GJF A 601 " both_signs ideal model delta sigma weight residual True 3.30 2.94 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" P2 GJF A 602 " pdb=" O5 GJF A 602 " pdb=" O6 GJF A 602 " pdb=" O9 GJF A 602 " both_signs ideal model delta sigma weight residual True 3.30 2.97 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 541 not shown) Planarity restraints: 549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 81 " 0.045 5.00e-02 4.00e+02 6.71e-02 7.21e+00 pdb=" N PRO A 82 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 380 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C VAL A 380 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL A 380 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO A 381 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 69 " 0.038 5.00e-02 4.00e+02 5.60e-02 5.01e+00 pdb=" N PRO A 70 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " 0.032 5.00e-02 4.00e+02 ... (remaining 546 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1152 2.84 - 3.35: 3057 3.35 - 3.87: 5650 3.87 - 4.38: 6913 4.38 - 4.90: 11150 Nonbonded interactions: 27922 Sorted by model distance: nonbonded pdb=" O LYS A 411 " pdb=" OG1 THR A 415 " model vdw 2.320 2.440 nonbonded pdb=" O THR A 408 " pdb=" OG1 THR A 412 " model vdw 2.370 2.440 nonbonded pdb=" O PHE A 276 " pdb=" OH TYR A 438 " model vdw 2.382 2.440 nonbonded pdb=" N ASP A 215 " pdb=" OD1 ASP A 215 " model vdw 2.399 2.520 nonbonded pdb=" N ASP A 19 " pdb=" OD1 ASP A 19 " model vdw 2.430 2.520 ... (remaining 27917 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: 1.170 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: 7.020 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.150 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.355 3403 Z= 0.747 Angle : 1.531 26.565 4658 Z= 0.655 Chirality : 0.063 0.367 544 Planarity : 0.006 0.067 549 Dihedral : 13.522 87.991 1150 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.26 % 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: -6.81 (0.22), residues: 396 helix: -4.60 (0.10), residues: 316 sheet: None (None), residues: 0 loop : -2.52 (0.57), residues: 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.367 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 77 average time/residue: 0.2415 time to fit residues: 21.4071 Evaluate side-chains 60 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0462 time to fit residues: 0.5856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 277 ASN A 289 HIS A 300 ASN A 377 GLN A 431 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 3403 Z= 0.230 Angle : 0.583 6.047 4658 Z= 0.291 Chirality : 0.039 0.179 544 Planarity : 0.005 0.037 549 Dihedral : 9.586 101.419 453 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 2.03 % 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: -3.76 (0.33), residues: 396 helix: -2.47 (0.22), residues: 310 sheet: None (None), residues: 0 loop : -1.53 (0.62), residues: 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.373 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 72 average time/residue: 0.2178 time to fit residues: 18.4038 Evaluate side-chains 56 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0386 time to fit residues: 0.7773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 3403 Z= 0.211 Angle : 0.531 7.293 4658 Z= 0.260 Chirality : 0.038 0.122 544 Planarity : 0.003 0.028 549 Dihedral : 9.265 95.749 453 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.39), residues: 396 helix: -0.96 (0.28), residues: 308 sheet: None (None), residues: 0 loop : -1.32 (0.61), residues: 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.404 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 64 average time/residue: 0.2236 time to fit residues: 16.6848 Evaluate side-chains 58 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0397 time to fit residues: 0.6880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.0970 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 3403 Z= 0.184 Angle : 0.510 6.092 4658 Z= 0.248 Chirality : 0.037 0.127 544 Planarity : 0.003 0.024 549 Dihedral : 9.105 94.944 453 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.41), residues: 396 helix: -0.24 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -1.29 (0.64), residues: 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.408 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 60 average time/residue: 0.2179 time to fit residues: 15.3357 Evaluate side-chains 55 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0378 time to fit residues: 0.6970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 3403 Z= 0.264 Angle : 0.541 6.020 4658 Z= 0.266 Chirality : 0.040 0.189 544 Planarity : 0.003 0.023 549 Dihedral : 9.229 95.407 453 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 0.29 % 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: -0.56 (0.42), residues: 396 helix: -0.09 (0.29), residues: 315 sheet: None (None), residues: 0 loop : -0.95 (0.69), residues: 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.394 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.2418 time to fit residues: 16.3275 Evaluate side-chains 53 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.343 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 chunk 37 optimal weight: 0.0270 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 277 ASN A 386 GLN A 403 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 3403 Z= 0.166 Angle : 0.490 5.824 4658 Z= 0.241 Chirality : 0.037 0.121 544 Planarity : 0.003 0.022 549 Dihedral : 9.045 93.468 453 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.42), residues: 396 helix: 0.27 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -1.01 (0.68), residues: 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.407 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 52 average time/residue: 0.2373 time to fit residues: 14.4953 Evaluate side-chains 52 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.378 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0389 time to fit residues: 0.5884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 3403 Z= 0.275 Angle : 0.543 6.162 4658 Z= 0.265 Chirality : 0.040 0.190 544 Planarity : 0.003 0.021 549 Dihedral : 9.193 94.670 453 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.42), residues: 396 helix: 0.33 (0.29), residues: 315 sheet: None (None), residues: 0 loop : -0.91 (0.70), residues: 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.420 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 60 average time/residue: 0.2155 time to fit residues: 15.2601 Evaluate side-chains 59 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0542 time to fit residues: 0.7652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.0470 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 3403 Z= 0.181 Angle : 0.500 5.516 4658 Z= 0.246 Chirality : 0.037 0.116 544 Planarity : 0.003 0.021 549 Dihedral : 9.094 94.285 453 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.43), residues: 396 helix: 0.60 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -1.03 (0.68), residues: 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.377 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 0.2278 time to fit residues: 15.0675 Evaluate side-chains 54 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0394 time to fit residues: 0.7192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 26 optimal weight: 0.0000 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 0.0870 chunk 24 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 overall best weight: 0.2762 ------------------------------------------------------------------------------- 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: 0.7447 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 3403 Z= 0.134 Angle : 0.487 5.827 4658 Z= 0.240 Chirality : 0.036 0.144 544 Planarity : 0.003 0.021 549 Dihedral : 8.828 91.709 453 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 0.29 % 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: 0.71 (0.43), residues: 396 helix: 0.94 (0.31), residues: 312 sheet: None (None), residues: 0 loop : -1.10 (0.66), residues: 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.374 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 0.2126 time to fit residues: 14.0328 Evaluate side-chains 53 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.371 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 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: 0.7506 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 3403 Z= 0.263 Angle : 0.540 5.662 4658 Z= 0.264 Chirality : 0.039 0.121 544 Planarity : 0.003 0.020 549 Dihedral : 9.090 93.984 453 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.00 % 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: 0.59 (0.43), residues: 396 helix: 0.80 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -0.92 (0.69), residues: 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.384 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2287 time to fit residues: 15.0536 Evaluate side-chains 54 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.373 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.128003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.112302 restraints weight = 4154.111| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.84 r_work: 0.3181 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 3403 Z= 0.206 Angle : 0.517 5.666 4658 Z= 0.254 Chirality : 0.038 0.116 544 Planarity : 0.003 0.022 549 Dihedral : 9.089 94.966 453 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.43), residues: 396 helix: 0.88 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -1.02 (0.68), residues: 82 =============================================================================== Job complete usr+sys time: 1210.59 seconds wall clock time: 22 minutes 26.16 seconds (1346.16 seconds total)