Starting phenix.real_space_refine on Wed Mar 5 17:47:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cv3_27007/03_2025/8cv3_27007.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cv3_27007/03_2025/8cv3_27007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cv3_27007/03_2025/8cv3_27007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cv3_27007/03_2025/8cv3_27007.map" model { file = "/net/cci-nas-00/data/ceres_data/8cv3_27007/03_2025/8cv3_27007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cv3_27007/03_2025/8cv3_27007.cif" } resolution = 3.04 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= 0.004 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 S 21 5.16 5 Na 2 4.78 5 C 2076 2.51 5 N 504 2.21 5 O 565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3168 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3166 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 11, 'TRANS': 404} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.82, per 1000 atoms: 0.89 Number of scatterers: 3168 At special positions: 0 Unit cell: (67.308, 61.344, 77.532, 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 21 16.00 Na 2 11.00 O 565 8.00 N 504 7.00 C 2076 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 365.1 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 85.3% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 removed outlier: 3.634A pdb=" N LEU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.694A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 82 removed outlier: 4.403A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.857A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 117 removed outlier: 3.594A pdb=" N ILE A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 148 Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.533A pdb=" N ALA A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 230 removed outlier: 3.629A pdb=" N LEU A 215 " --> pdb=" O ASN A 211 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 273 removed outlier: 3.556A pdb=" N VAL A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 4.285A pdb=" N VAL A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 282 through 299 removed outlier: 3.554A pdb=" N VAL A 289 " --> pdb=" O TYR A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.755A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.794A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 390 through 404 Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.716A pdb=" N VAL A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 437 removed outlier: 4.252A pdb=" N ILE A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 4.717A pdb=" N ARG A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 removed outlier: 3.782A pdb=" N VAL A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 242 hydrogen bonds defined for protein. 723 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: 0.83 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 946 1.34 - 1.45: 356 1.45 - 1.57: 1872 1.57 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 3213 Sorted by residual: bond pdb=" N ILE A 421 " pdb=" CA ILE A 421 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.46e+00 bond pdb=" N VAL A 411 " pdb=" CA VAL A 411 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.23e-02 6.61e+03 7.18e+00 bond pdb=" N GLY A 410 " pdb=" CA GLY A 410 " ideal model delta sigma weight residual 1.447 1.476 -0.028 1.58e-02 4.01e+03 3.21e+00 bond pdb=" C GLN A 413 " pdb=" O GLN A 413 " ideal model delta sigma weight residual 1.234 1.255 -0.021 1.20e-02 6.94e+03 3.13e+00 bond pdb=" CB GLN A 413 " pdb=" CG GLN A 413 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.75e+00 ... (remaining 3208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 4281 1.56 - 3.11: 57 3.11 - 4.67: 14 4.67 - 6.22: 4 6.22 - 7.78: 4 Bond angle restraints: 4360 Sorted by residual: angle pdb=" CA GLN A 413 " pdb=" CB GLN A 413 " pdb=" CG GLN A 413 " ideal model delta sigma weight residual 114.10 120.85 -6.75 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CA PRO A 412 " pdb=" C PRO A 412 " pdb=" O PRO A 412 " ideal model delta sigma weight residual 121.77 118.13 3.64 1.14e+00 7.69e-01 1.02e+01 angle pdb=" CA ILE A 421 " pdb=" C ILE A 421 " pdb=" O ILE A 421 " ideal model delta sigma weight residual 121.17 118.11 3.06 1.06e+00 8.90e-01 8.35e+00 angle pdb=" CB LEU A 265 " pdb=" CG LEU A 265 " pdb=" CD1 LEU A 265 " ideal model delta sigma weight residual 110.70 103.30 7.40 3.00e+00 1.11e-01 6.08e+00 angle pdb=" O ILE A 421 " pdb=" C ILE A 421 " pdb=" N VAL A 422 " ideal model delta sigma weight residual 121.91 124.32 -2.41 9.80e-01 1.04e+00 6.06e+00 ... (remaining 4355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.87: 1592 11.87 - 23.75: 209 23.75 - 35.62: 82 35.62 - 47.49: 23 47.49 - 59.36: 15 Dihedral angle restraints: 1921 sinusoidal: 728 harmonic: 1193 Sorted by residual: dihedral pdb=" CA ASP A 351 " pdb=" CB ASP A 351 " pdb=" CG ASP A 351 " pdb=" OD1 ASP A 351 " ideal model delta sinusoidal sigma weight residual -30.00 -83.34 53.34 1 2.00e+01 2.50e-03 9.67e+00 dihedral pdb=" CB ARG A 445 " pdb=" CG ARG A 445 " pdb=" CD ARG A 445 " pdb=" NE ARG A 445 " ideal model delta sinusoidal sigma weight residual 60.00 119.36 -59.36 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CG LYS A 201 " pdb=" CD LYS A 201 " pdb=" CE LYS A 201 " pdb=" NZ LYS A 201 " ideal model delta sinusoidal sigma weight residual 60.00 1.95 58.05 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 403 0.038 - 0.076: 120 0.076 - 0.114: 26 0.114 - 0.152: 2 0.152 - 0.190: 2 Chirality restraints: 553 Sorted by residual: chirality pdb=" CA ILE A 421 " pdb=" N ILE A 421 " pdb=" C ILE A 421 " pdb=" CB ILE A 421 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA VAL A 411 " pdb=" N VAL A 411 " pdb=" C VAL A 411 " pdb=" CB VAL A 411 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA MET A 367 " pdb=" N MET A 367 " pdb=" C MET A 367 " pdb=" CB MET A 367 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 550 not shown) Planarity restraints: 531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 417 " -0.026 2.00e-02 2.50e+03 5.13e-02 2.63e+01 pdb=" C VAL A 417 " 0.089 2.00e-02 2.50e+03 pdb=" O VAL A 417 " -0.033 2.00e-02 2.50e+03 pdb=" N THR A 418 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 326 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C THR A 326 " 0.028 2.00e-02 2.50e+03 pdb=" O THR A 326 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA A 327 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 258 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO A 259 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " -0.022 5.00e-02 4.00e+02 ... (remaining 528 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 933 2.83 - 3.35: 3144 3.35 - 3.86: 4984 3.86 - 4.38: 5450 4.38 - 4.90: 9882 Nonbonded interactions: 24393 Sorted by model distance: nonbonded pdb=" O THR A 336 " pdb=" OG1 THR A 340 " model vdw 2.310 3.040 nonbonded pdb=" O PRO A 69 " pdb=" OG SER A 73 " model vdw 2.323 3.040 nonbonded pdb=" OD1 ASP A 368 " pdb="NA NA A 602 " model vdw 2.366 2.470 nonbonded pdb=" OG1 THR A 101 " pdb="NA NA A 602 " model vdw 2.386 2.470 nonbonded pdb=" O THR A 396 " pdb=" OG1 THR A 400 " model vdw 2.396 3.040 ... (remaining 24388 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: 1.490 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.760 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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 0.050 3213 Z= 0.198 Angle : 0.513 7.776 4360 Z= 0.277 Chirality : 0.038 0.190 553 Planarity : 0.004 0.051 531 Dihedral : 14.071 59.364 1151 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 19.60 % Favored : 80.40 % 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: 1.93 (0.42), residues: 410 helix: 1.97 (0.29), residues: 325 sheet: 0.18 (1.38), residues: 18 loop : -1.91 (0.65), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 276 HIS 0.000 0.000 HIS A 296 PHE 0.003 0.000 PHE A 14 TYR 0.012 0.001 TYR A 200 ARG 0.001 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.368 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1336 time to fit residues: 8.4288 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.152169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.118419 restraints weight = 3763.105| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.60 r_work: 0.3137 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3213 Z= 0.168 Angle : 0.467 7.096 4360 Z= 0.248 Chirality : 0.037 0.131 553 Planarity : 0.004 0.066 531 Dihedral : 3.636 15.460 436 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.02 % Allowed : 17.00 % Favored : 80.98 % 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: 2.56 (0.42), residues: 410 helix: 2.39 (0.28), residues: 327 sheet: 0.37 (1.44), residues: 18 loop : -1.66 (0.66), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 PHE 0.008 0.001 PHE A 240 TYR 0.007 0.001 TYR A 305 ARG 0.001 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5800 (OUTLIER) cc_final: 0.5261 (tp) REVERT: A 255 MET cc_start: 0.8516 (mmt) cc_final: 0.8108 (mmt) outliers start: 7 outliers final: 3 residues processed: 50 average time/residue: 0.1179 time to fit residues: 7.6596 Evaluate side-chains 48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 0.0970 chunk 30 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.153275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.120205 restraints weight = 3696.486| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.56 r_work: 0.3152 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3213 Z= 0.169 Angle : 0.456 6.632 4360 Z= 0.242 Chirality : 0.036 0.133 553 Planarity : 0.004 0.068 531 Dihedral : 3.613 14.969 436 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.73 % Allowed : 19.31 % Favored : 78.96 % 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: 2.63 (0.42), residues: 410 helix: 2.45 (0.28), residues: 327 sheet: 0.34 (1.41), residues: 18 loop : -1.71 (0.64), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.001 0.000 HIS A 41 PHE 0.009 0.001 PHE A 240 TYR 0.005 0.001 TYR A 97 ARG 0.001 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8505 (mmt) cc_final: 0.8127 (mmt) outliers start: 6 outliers final: 3 residues processed: 50 average time/residue: 0.1158 time to fit residues: 7.6055 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.0170 overall best weight: 0.4018 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.153879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.120346 restraints weight = 3748.543| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.62 r_work: 0.3200 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3213 Z= 0.144 Angle : 0.431 6.450 4360 Z= 0.228 Chirality : 0.036 0.128 553 Planarity : 0.004 0.070 531 Dihedral : 3.528 14.432 436 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.44 % Allowed : 18.16 % Favored : 80.40 % 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: 2.91 (0.42), residues: 410 helix: 2.66 (0.28), residues: 327 sheet: 0.34 (1.41), residues: 18 loop : -1.73 (0.64), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 276 HIS 0.001 0.000 HIS A 41 PHE 0.006 0.001 PHE A 264 TYR 0.004 0.001 TYR A 97 ARG 0.001 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5805 (OUTLIER) cc_final: 0.5240 (tp) REVERT: A 255 MET cc_start: 0.8418 (mmt) cc_final: 0.8089 (mmt) REVERT: A 262 ILE cc_start: 0.7948 (mm) cc_final: 0.7724 (mt) outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 0.1161 time to fit residues: 7.4732 Evaluate side-chains 48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.149509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.114663 restraints weight = 3774.357| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.65 r_work: 0.3131 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3213 Z= 0.202 Angle : 0.474 6.680 4360 Z= 0.251 Chirality : 0.037 0.134 553 Planarity : 0.004 0.071 531 Dihedral : 3.598 15.719 436 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.02 % Allowed : 17.29 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.42), residues: 410 helix: 2.47 (0.28), residues: 327 sheet: 0.30 (1.40), residues: 18 loop : -1.83 (0.63), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 256 HIS 0.001 0.001 HIS A 41 PHE 0.013 0.001 PHE A 240 TYR 0.005 0.001 TYR A 97 ARG 0.001 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8557 (mmt) cc_final: 0.8277 (mmt) REVERT: A 262 ILE cc_start: 0.8032 (mm) cc_final: 0.7827 (mt) outliers start: 7 outliers final: 5 residues processed: 50 average time/residue: 0.1199 time to fit residues: 7.8990 Evaluate side-chains 50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 391 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 32 optimal weight: 0.0060 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.152450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.118287 restraints weight = 3873.131| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.65 r_work: 0.3153 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3213 Z= 0.153 Angle : 0.438 6.351 4360 Z= 0.232 Chirality : 0.036 0.131 553 Planarity : 0.004 0.059 531 Dihedral : 3.547 15.002 436 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.31 % Allowed : 17.00 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.42), residues: 410 helix: 2.64 (0.28), residues: 326 sheet: 0.20 (1.40), residues: 18 loop : -1.91 (0.62), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.001 0.000 HIS A 41 PHE 0.007 0.001 PHE A 240 TYR 0.005 0.001 TYR A 305 ARG 0.001 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5606 (OUTLIER) cc_final: 0.5207 (tp) REVERT: A 255 MET cc_start: 0.8323 (mmt) cc_final: 0.7978 (mmt) REVERT: A 262 ILE cc_start: 0.7759 (mm) cc_final: 0.7486 (mt) outliers start: 8 outliers final: 5 residues processed: 50 average time/residue: 0.1180 time to fit residues: 7.8319 Evaluate side-chains 48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 391 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 0.0070 chunk 37 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.155017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.121608 restraints weight = 3776.701| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.61 r_work: 0.3147 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3213 Z= 0.168 Angle : 0.466 9.194 4360 Z= 0.242 Chirality : 0.037 0.131 553 Planarity : 0.004 0.053 531 Dihedral : 3.545 15.186 436 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.59 % Allowed : 16.43 % Favored : 80.98 % 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: 2.74 (0.42), residues: 410 helix: 2.59 (0.28), residues: 326 sheet: 0.05 (1.37), residues: 18 loop : -1.90 (0.62), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 19 HIS 0.001 0.000 HIS A 41 PHE 0.010 0.001 PHE A 240 TYR 0.005 0.001 TYR A 97 ARG 0.001 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5818 (OUTLIER) cc_final: 0.5402 (tp) REVERT: A 41 HIS cc_start: 0.6815 (m90) cc_final: 0.6541 (m170) REVERT: A 262 ILE cc_start: 0.7901 (mm) cc_final: 0.7649 (mt) outliers start: 9 outliers final: 5 residues processed: 51 average time/residue: 0.1199 time to fit residues: 8.0139 Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 391 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.0870 chunk 21 optimal weight: 0.0060 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 0.0000 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.157444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.124544 restraints weight = 3767.968| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.61 r_work: 0.3184 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3213 Z= 0.146 Angle : 0.454 9.144 4360 Z= 0.234 Chirality : 0.036 0.129 553 Planarity : 0.004 0.050 531 Dihedral : 3.483 14.537 436 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.31 % Allowed : 16.71 % Favored : 80.98 % 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: 2.91 (0.42), residues: 410 helix: 2.72 (0.29), residues: 326 sheet: 0.17 (1.38), residues: 18 loop : -1.90 (0.63), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 19 HIS 0.001 0.000 HIS A 41 PHE 0.007 0.001 PHE A 264 TYR 0.004 0.001 TYR A 97 ARG 0.001 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5360 (tp) REVERT: A 41 HIS cc_start: 0.6756 (m90) cc_final: 0.6518 (m170) REVERT: A 255 MET cc_start: 0.8376 (mmt) cc_final: 0.8043 (mmt) REVERT: A 262 ILE cc_start: 0.7859 (mm) cc_final: 0.7603 (mt) outliers start: 8 outliers final: 5 residues processed: 47 average time/residue: 0.1128 time to fit residues: 7.1243 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 391 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.150952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.116202 restraints weight = 3779.456| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.65 r_work: 0.3141 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3213 Z= 0.181 Angle : 0.487 9.082 4360 Z= 0.249 Chirality : 0.037 0.132 553 Planarity : 0.004 0.048 531 Dihedral : 3.527 15.250 436 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.02 % Allowed : 17.29 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.42), residues: 410 helix: 2.58 (0.28), residues: 326 sheet: 0.12 (1.37), residues: 18 loop : -1.91 (0.62), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 256 HIS 0.001 0.000 HIS A 41 PHE 0.011 0.001 PHE A 240 TYR 0.005 0.001 TYR A 97 ARG 0.002 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5810 (OUTLIER) cc_final: 0.5394 (tp) REVERT: A 41 HIS cc_start: 0.6836 (m90) cc_final: 0.6613 (m170) REVERT: A 262 ILE cc_start: 0.7960 (mm) cc_final: 0.7723 (mt) REVERT: A 373 TYR cc_start: 0.6430 (t80) cc_final: 0.5752 (t80) outliers start: 7 outliers final: 5 residues processed: 52 average time/residue: 0.1130 time to fit residues: 7.8439 Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 391 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 0.0170 chunk 33 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.158412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.126573 restraints weight = 3686.302| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.52 r_work: 0.3205 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3213 Z= 0.154 Angle : 0.462 9.044 4360 Z= 0.238 Chirality : 0.036 0.130 553 Planarity : 0.004 0.048 531 Dihedral : 3.490 14.663 436 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.73 % Allowed : 17.58 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.42), residues: 410 helix: 2.70 (0.29), residues: 326 sheet: 0.17 (1.37), residues: 18 loop : -1.97 (0.61), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 276 HIS 0.001 0.000 HIS A 41 PHE 0.007 0.001 PHE A 264 TYR 0.008 0.001 TYR A 305 ARG 0.001 0.000 ARG A 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5812 (OUTLIER) cc_final: 0.5375 (tp) REVERT: A 255 MET cc_start: 0.8410 (mmt) cc_final: 0.8034 (mmt) REVERT: A 262 ILE cc_start: 0.7957 (mm) cc_final: 0.7709 (mt) REVERT: A 373 TYR cc_start: 0.6373 (t80) cc_final: 0.5720 (t80) outliers start: 6 outliers final: 5 residues processed: 49 average time/residue: 0.1170 time to fit residues: 7.6445 Evaluate side-chains 50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 391 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.149496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.114008 restraints weight = 3780.635| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.69 r_work: 0.3103 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3213 Z= 0.206 Angle : 0.502 9.099 4360 Z= 0.261 Chirality : 0.038 0.153 553 Planarity : 0.004 0.048 531 Dihedral : 3.580 15.701 436 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.73 % Allowed : 18.73 % Favored : 79.54 % 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: 2.59 (0.42), residues: 410 helix: 2.48 (0.28), residues: 326 sheet: 1.01 (1.32), residues: 16 loop : -2.17 (0.60), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 256 HIS 0.002 0.001 HIS A 41 PHE 0.013 0.001 PHE A 240 TYR 0.009 0.001 TYR A 305 ARG 0.001 0.000 ARG A 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2006.44 seconds wall clock time: 35 minutes 5.25 seconds (2105.25 seconds total)