Starting phenix.real_space_refine on Mon Feb 10 22:46:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cv3_27007/02_2025/8cv3_27007.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cv3_27007/02_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_27007/02_2025/8cv3_27007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cv3_27007/02_2025/8cv3_27007.map" model { file = "/net/cci-nas-00/data/ceres_data/8cv3_27007/02_2025/8cv3_27007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cv3_27007/02_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-5592/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: 2.60, per 1000 atoms: 0.82 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: 0.78 Conformation dependent library (CDL) restraints added in 436.3 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: 0.33 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: 0.91 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 1.090 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: 0.030 Process input model: 12.260 Find NCS groups from input model: 0.030 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.540 ------------------------------------------------------------------------------- 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 : 0.350 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1370 time to fit residues: 8.6561 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 : 0.425 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.118452 restraints weight = 3763.115| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.59 r_work: 0.3139 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- 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 : 0.344 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.5265 (tp) REVERT: A 255 MET cc_start: 0.8517 (mmt) cc_final: 0.8111 (mmt) outliers start: 7 outliers final: 3 residues processed: 50 average time/residue: 0.1161 time to fit residues: 7.6087 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 : 0.338 ------------------------------------------------------------------------------- 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: 2.9990 chunk 21 optimal weight: 0.3980 chunk 30 optimal weight: 5.9990 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: 0.6980 chunk 35 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.153368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120286 restraints weight = 3696.951| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.56 r_work: 0.3161 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3213 Z= 0.170 Angle : 0.455 6.648 4360 Z= 0.242 Chirality : 0.036 0.132 553 Planarity : 0.004 0.069 531 Dihedral : 3.613 14.990 436 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.73 % Allowed : 19.02 % Favored : 79.25 % 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: 0.33 (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 276 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 : 0.369 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8530 (mmt) cc_final: 0.8177 (mmt) outliers start: 6 outliers final: 3 residues processed: 50 average time/residue: 0.1234 time to fit residues: 8.1711 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 : 0.370 ------------------------------------------------------------------------------- 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: 0.9990 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.150377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.116137 restraints weight = 3759.081| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.62 r_work: 0.3145 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1350 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= 0.179 Angle : 0.459 6.661 4360 Z= 0.245 Chirality : 0.036 0.133 553 Planarity : 0.004 0.068 531 Dihedral : 3.626 15.366 436 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.31 % Allowed : 18.16 % 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: 2.67 (0.42), residues: 410 helix: 2.49 (0.28), residues: 327 sheet: 0.26 (1.41), residues: 18 loop : -1.73 (0.65), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 276 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 0.001 0.000 ARG A 447 *********************** 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 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5889 (OUTLIER) cc_final: 0.5354 (tp) REVERT: A 255 MET cc_start: 0.8531 (mmt) cc_final: 0.8150 (mmt) REVERT: A 262 ILE cc_start: 0.8028 (mm) cc_final: 0.7827 (mt) outliers start: 8 outliers final: 5 residues processed: 52 average time/residue: 0.1209 time to fit residues: 8.3094 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 : 0.353 ------------------------------------------------------------------------------- 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=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: 0.8980 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.149097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.114152 restraints weight = 3771.478| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.66 r_work: 0.3103 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3213 Z= 0.193 Angle : 0.467 6.630 4360 Z= 0.249 Chirality : 0.037 0.135 553 Planarity : 0.004 0.056 531 Dihedral : 3.651 15.759 436 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.02 % Allowed : 17.87 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.42), residues: 410 helix: 2.46 (0.28), residues: 327 sheet: 1.18 (1.38), residues: 16 loop : -2.01 (0.62), residues: 67 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 0.012 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 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5951 (OUTLIER) cc_final: 0.5352 (tp) REVERT: A 255 MET cc_start: 0.8504 (mmt) cc_final: 0.8199 (mmt) REVERT: A 262 ILE cc_start: 0.7970 (mm) cc_final: 0.7745 (mt) REVERT: A 373 TYR cc_start: 0.6479 (t80) cc_final: 0.5749 (t80) outliers start: 7 outliers final: 5 residues processed: 52 average time/residue: 0.1172 time to fit residues: 8.0455 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 : 0.363 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 32 optimal weight: 0.0470 chunk 34 optimal weight: 0.0970 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.154999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.121268 restraints weight = 3870.401| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.65 r_work: 0.3174 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 3213 Z= 0.149 Angle : 0.434 6.315 4360 Z= 0.230 Chirality : 0.036 0.130 553 Planarity : 0.004 0.073 531 Dihedral : 3.553 14.770 436 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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: 2.88 (0.42), residues: 410 helix: 2.70 (0.28), residues: 326 sheet: 0.14 (1.40), residues: 18 loop : -1.93 (0.61), 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 0.006 0.001 PHE A 264 TYR 0.005 0.001 TYR A 305 ARG 0.001 0.000 ARG A 61 *********************** 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 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5796 (OUTLIER) cc_final: 0.5209 (tp) REVERT: A 255 MET cc_start: 0.8395 (mmt) cc_final: 0.8035 (mmt) REVERT: A 262 ILE cc_start: 0.7870 (mm) cc_final: 0.7610 (mt) REVERT: A 373 TYR cc_start: 0.6415 (t80) cc_final: 0.5746 (t80) outliers start: 8 outliers final: 4 residues processed: 52 average time/residue: 0.1203 time to fit residues: 8.1387 Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 0.0570 chunk 37 optimal weight: 0.1980 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: 2.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.150117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.115240 restraints weight = 3785.117| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.65 r_work: 0.3129 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1482 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= 0.193 Angle : 0.478 9.350 4360 Z= 0.250 Chirality : 0.037 0.133 553 Planarity : 0.004 0.063 531 Dihedral : 3.579 15.504 436 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.88 % Allowed : 16.71 % 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: 2.67 (0.42), residues: 410 helix: 2.54 (0.28), residues: 326 sheet: 0.08 (1.39), residues: 18 loop : -1.93 (0.61), 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 0.012 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: 10 poor density : 43 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 262 ILE cc_start: 0.7931 (mm) cc_final: 0.7685 (mt) REVERT: A 373 TYR cc_start: 0.6437 (t80) cc_final: 0.5749 (t80) outliers start: 10 outliers final: 6 residues processed: 51 average time/residue: 0.1267 time to fit residues: 8.6273 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 : 0.374 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 0.0000 chunk 21 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 32 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.4762 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.152054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.117515 restraints weight = 3760.443| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.68 r_work: 0.3151 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 3213 Z= 0.155 Angle : 0.462 9.225 4360 Z= 0.238 Chirality : 0.036 0.131 553 Planarity : 0.004 0.058 531 Dihedral : 3.536 14.749 436 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.37 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: 2.83 (0.42), residues: 410 helix: 2.67 (0.28), residues: 326 sheet: 0.03 (1.37), residues: 18 loop : -1.97 (0.60), residues: 66 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 0.007 0.001 PHE A 240 TYR 0.008 0.001 TYR A 305 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: 7 poor density : 42 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5676 (OUTLIER) cc_final: 0.5255 (tp) REVERT: A 41 HIS cc_start: 0.6755 (m90) cc_final: 0.6471 (m170) REVERT: A 255 MET cc_start: 0.8342 (mmt) cc_final: 0.7937 (mmt) REVERT: A 262 ILE cc_start: 0.7878 (mm) cc_final: 0.7627 (mt) REVERT: A 373 TYR cc_start: 0.6353 (t80) cc_final: 0.5680 (t80) outliers start: 7 outliers final: 5 residues processed: 47 average time/residue: 0.1094 time to fit residues: 6.8574 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 : 0.362 ------------------------------------------------------------------------------- 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 475 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.149801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.114417 restraints weight = 3789.233| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.70 r_work: 0.3117 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1540 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= 0.191 Angle : 0.495 9.298 4360 Z= 0.253 Chirality : 0.037 0.133 553 Planarity : 0.004 0.056 531 Dihedral : 3.597 15.755 436 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.31 % Allowed : 17.29 % 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: 2.61 (0.42), residues: 410 helix: 2.51 (0.28), residues: 326 sheet: -0.03 (1.35), residues: 18 loop : -1.98 (0.60), 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 0.012 0.001 PHE A 240 TYR 0.008 0.001 TYR A 305 ARG 0.001 0.000 ARG A 447 *********************** 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 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5801 (OUTLIER) cc_final: 0.5424 (tp) REVERT: A 41 HIS cc_start: 0.6836 (m90) cc_final: 0.6589 (m170) REVERT: A 373 TYR cc_start: 0.6454 (t80) cc_final: 0.5749 (t80) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 0.1183 time to fit residues: 7.8736 Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.150293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.115370 restraints weight = 3706.075| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.64 r_work: 0.3128 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3213 Z= 0.186 Angle : 0.486 8.383 4360 Z= 0.251 Chirality : 0.037 0.133 553 Planarity : 0.004 0.055 531 Dihedral : 3.603 15.432 436 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.37 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: 2.61 (0.42), residues: 410 helix: 2.51 (0.28), residues: 326 sheet: -0.07 (1.35), residues: 18 loop : -2.01 (0.60), residues: 66 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 0.010 0.001 PHE A 240 TYR 0.008 0.001 TYR A 305 ARG 0.001 0.000 ARG A 447 ********************** 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: 7 poor density : 44 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5777 (OUTLIER) cc_final: 0.5402 (tp) REVERT: A 41 HIS cc_start: 0.6837 (m90) cc_final: 0.6595 (m170) REVERT: A 373 TYR cc_start: 0.6408 (t80) cc_final: 0.5700 (t80) outliers start: 7 outliers final: 5 residues processed: 49 average time/residue: 0.1098 time to fit residues: 7.2120 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 : 0.271 ------------------------------------------------------------------------------- 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 269 CYS Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.149161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.113974 restraints weight = 3787.097| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.66 r_work: 0.3104 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3213 Z= 0.201 Angle : 0.507 10.672 4360 Z= 0.260 Chirality : 0.037 0.134 553 Planarity : 0.004 0.054 531 Dihedral : 3.643 15.920 436 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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: 2.51 (0.42), residues: 410 helix: 2.44 (0.28), residues: 326 sheet: -0.10 (1.34), residues: 18 loop : -2.01 (0.60), 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 0.012 0.001 PHE A 240 TYR 0.008 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: 1937.91 seconds wall clock time: 35 minutes 6.28 seconds (2106.28 seconds total)