Starting phenix.real_space_refine on Mon Feb 10 23:11:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ugj_26489/02_2025/7ugj_26489.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ugj_26489/02_2025/7ugj_26489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ugj_26489/02_2025/7ugj_26489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ugj_26489/02_2025/7ugj_26489.map" model { file = "/net/cci-nas-00/data/ceres_data/7ugj_26489/02_2025/7ugj_26489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ugj_26489/02_2025/7ugj_26489.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.036 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: 6 Type Number sf(0) Gaussians S 16 5.16 5 Na 2 4.78 5 C 2035 2.51 5 N 504 2.21 5 O 537 1.98 5 F 1 1.80 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: 3095 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3076 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 397} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'EFC:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {' NA': 2, 'TB1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.00, per 1000 atoms: 0.97 Number of scatterers: 3095 At special positions: 0 Unit cell: (63.9, 79.236, 83.496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 16 16.00 Na 2 11.00 F 1 9.00 O 537 8.00 N 504 7.00 C 2035 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: 0.95 Conformation dependent library (CDL) restraints added in 454.5 milliseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 90.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 removed outlier: 4.251A pdb=" N LYS A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 8 " --> pdb=" O TYR A 4 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 10 " --> pdb=" O LYS A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 33 Processing helix chain 'A' and resid 35 through 57 removed outlier: 4.197A pdb=" N LYS A 44 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 3.663A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 73 Processing helix chain 'A' and resid 74 through 108 removed outlier: 3.552A pdb=" N ARG A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 141 through 149 removed outlier: 3.591A pdb=" N LEU A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 170 removed outlier: 3.506A pdb=" N THR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 221 removed outlier: 3.645A pdb=" N GLY A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 222 through 226 removed outlier: 3.579A pdb=" N VAL A 225 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLY A 226 " --> pdb=" O HIS A 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 222 through 226' Processing helix chain 'A' and resid 227 through 246 removed outlier: 3.719A pdb=" N VAL A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 254 Processing helix chain 'A' and resid 257 through 265 removed outlier: 3.614A pdb=" N HIS A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 276 removed outlier: 3.551A pdb=" N PHE A 273 " --> pdb=" O MET A 269 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 293 Proline residue: A 283 - end of helix removed outlier: 3.538A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 4.144A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 303 " --> pdb=" O TYR A 299 " (cutoff:3.500A) Proline residue: A 304 - end of helix removed outlier: 3.712A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 330 removed outlier: 3.759A pdb=" N PHE A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.550A pdb=" N VAL A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 370 removed outlier: 4.062A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 387 removed outlier: 3.779A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 387 " --> pdb=" O TYR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 417 removed outlier: 3.885A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 735 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: 0.84 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 983 1.37 - 1.55: 2141 1.55 - 1.73: 0 1.73 - 1.92: 30 1.92 - 2.10: 1 Bond restraints: 3155 Sorted by residual: bond pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 2.054 2.101 -0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" C EFC A 385 " pdb=" O EFC A 385 " ideal model delta sigma weight residual 1.231 1.185 0.046 2.00e-02 2.50e+03 5.20e+00 bond pdb=" C1 TB1 A 501 " pdb=" C4 TB1 A 501 " ideal model delta sigma weight residual 1.503 1.528 -0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" C2 EFC A 385 " pdb=" F2 EFC A 385 " ideal model delta sigma weight residual 1.388 1.364 0.024 2.00e-02 2.50e+03 1.40e+00 bond pdb=" C1 EFC A 385 " pdb=" C2 EFC A 385 " ideal model delta sigma weight residual 1.506 1.526 -0.020 2.00e-02 2.50e+03 1.05e+00 ... (remaining 3150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 4254 1.79 - 3.58: 33 3.58 - 5.36: 12 5.36 - 7.15: 3 7.15 - 8.94: 1 Bond angle restraints: 4303 Sorted by residual: angle pdb=" CB EFC A 385 " pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 101.65 110.59 -8.94 3.00e+00 1.11e-01 8.88e+00 angle pdb=" C LEU A 245 " pdb=" N VAL A 246 " pdb=" CA VAL A 246 " ideal model delta sigma weight residual 122.97 120.65 2.32 9.80e-01 1.04e+00 5.63e+00 angle pdb=" O1 TB1 A 501 " pdb=" C9 TB1 A 501 " pdb=" O5 TB1 A 501 " ideal model delta sigma weight residual 126.71 119.71 7.00 3.00e+00 1.11e-01 5.44e+00 angle pdb=" O3 TB1 A 501 " pdb=" C10 TB1 A 501 " pdb=" O4 TB1 A 501 " ideal model delta sigma weight residual 126.45 119.88 6.57 3.00e+00 1.11e-01 4.80e+00 angle pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " pdb=" C1 EFC A 385 " ideal model delta sigma weight residual 103.98 110.34 -6.36 3.00e+00 1.11e-01 4.50e+00 ... (remaining 4298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 1749 17.49 - 34.98: 82 34.98 - 52.47: 14 52.47 - 69.96: 3 69.96 - 87.46: 2 Dihedral angle restraints: 1850 sinusoidal: 672 harmonic: 1178 Sorted by residual: dihedral pdb=" CB MET A 59 " pdb=" CG MET A 59 " pdb=" SD MET A 59 " pdb=" CE MET A 59 " ideal model delta sinusoidal sigma weight residual 180.00 122.19 57.81 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CB MET A 194 " pdb=" CG MET A 194 " pdb=" SD MET A 194 " pdb=" CE MET A 194 " ideal model delta sinusoidal sigma weight residual 180.00 123.09 56.91 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA ARG A 105 " pdb=" CB ARG A 105 " pdb=" CG ARG A 105 " pdb=" CD ARG A 105 " ideal model delta sinusoidal sigma weight residual -180.00 -135.03 -44.97 3 1.50e+01 4.44e-03 8.09e+00 ... (remaining 1847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 344 0.028 - 0.055: 127 0.055 - 0.083: 45 0.083 - 0.111: 19 0.111 - 0.138: 2 Chirality restraints: 537 Sorted by residual: chirality pdb=" C7 TB1 A 501 " pdb=" N TB1 A 501 " pdb=" C10 TB1 A 501 " pdb=" C11 TB1 A 501 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA PRO A 45 " pdb=" N PRO A 45 " pdb=" C PRO A 45 " pdb=" CB PRO A 45 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.13e-01 chirality pdb=" CA MET A 59 " pdb=" N MET A 59 " pdb=" C MET A 59 " pdb=" CB MET A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.66e-01 ... (remaining 534 not shown) Planarity restraints: 532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO A 45 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 355 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO A 356 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 356 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 356 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 376 " 0.016 5.00e-02 4.00e+02 2.38e-02 9.04e-01 pdb=" N PRO A 377 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 377 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 377 " 0.013 5.00e-02 4.00e+02 ... (remaining 529 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 824 2.81 - 3.33: 3277 3.33 - 3.85: 4667 3.85 - 4.38: 5570 4.38 - 4.90: 9580 Nonbonded interactions: 23918 Sorted by model distance: nonbonded pdb=" N TB1 A 501 " pdb=" O1 TB1 A 501 " model vdw 2.285 3.120 nonbonded pdb=" OG1 THR A 92 " pdb="NA NA A 503 " model vdw 2.348 2.470 nonbonded pdb=" OD1 ASN A 378 " pdb=" N VAL A 379 " model vdw 2.414 3.120 nonbonded pdb=" O VAL A 346 " pdb=" OG SER A 349 " model vdw 2.444 3.040 nonbonded pdb=" O ASN A 401 " pdb="NA NA A 502 " model vdw 2.463 2.470 ... (remaining 23913 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.630 Find NCS groups from input model: 0.020 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:13.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 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 : 0.002 0.047 3155 Z= 0.159 Angle : 0.498 8.940 4303 Z= 0.234 Chirality : 0.035 0.138 537 Planarity : 0.003 0.030 532 Dihedral : 10.716 87.456 1104 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 2.01 (0.39), residues: 411 helix: 1.51 (0.26), residues: 331 sheet: None (None), residues: 0 loop : 0.92 (0.75), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 219 PHE 0.005 0.001 PHE A 261 TYR 0.008 0.001 TYR A 7 ARG 0.002 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.355 Fit side-chains REVERT: A 108 ASN cc_start: 0.8987 (t0) cc_final: 0.8729 (t0) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 1.1481 time to fit residues: 62.7988 Evaluate side-chains 33 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.0770 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.109788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.074597 restraints weight = 5825.327| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.39 r_work: 0.2951 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3155 Z= 0.214 Angle : 0.588 5.177 4303 Z= 0.327 Chirality : 0.040 0.162 537 Planarity : 0.005 0.045 532 Dihedral : 7.606 66.575 459 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.27 % Allowed : 7.30 % Favored : 91.43 % 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: 2.94 (0.39), residues: 411 helix: 2.25 (0.26), residues: 350 sheet: None (None), residues: 0 loop : 0.16 (0.76), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 219 PHE 0.009 0.001 PHE A 323 TYR 0.013 0.002 TYR A 299 ARG 0.004 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.312 Fit side-chains REVERT: A 48 ASP cc_start: 0.8660 (m-30) cc_final: 0.8424 (m-30) outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 1.2433 time to fit residues: 56.4233 Evaluate side-chains 36 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 416 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.112163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.076294 restraints weight = 5617.571| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.43 r_work: 0.2953 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3155 Z= 0.196 Angle : 0.527 6.654 4303 Z= 0.278 Chirality : 0.038 0.175 537 Planarity : 0.004 0.047 532 Dihedral : 6.909 60.948 459 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.54 % Allowed : 12.70 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.41), residues: 411 helix: 2.36 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.01 (0.79), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 368 PHE 0.008 0.001 PHE A 323 TYR 0.008 0.001 TYR A 236 ARG 0.003 0.001 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.320 Fit side-chains REVERT: A 394 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7717 (t70) outliers start: 8 outliers final: 4 residues processed: 46 average time/residue: 1.2199 time to fit residues: 57.8324 Evaluate side-chains 38 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 416 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.112242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.075941 restraints weight = 5726.000| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.38 r_work: 0.2979 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3155 Z= 0.208 Angle : 0.537 6.381 4303 Z= 0.279 Chirality : 0.038 0.185 537 Planarity : 0.004 0.045 532 Dihedral : 6.708 60.127 459 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.22 % Allowed : 13.65 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.41), residues: 411 helix: 2.39 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.26 (0.79), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.006 0.001 PHE A 156 TYR 0.011 0.001 TYR A 299 ARG 0.003 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.335 Fit side-chains REVERT: A 48 ASP cc_start: 0.8601 (m-30) cc_final: 0.8336 (m-30) outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 1.2795 time to fit residues: 57.9508 Evaluate side-chains 42 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 416 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.110907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.075061 restraints weight = 5741.515| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.43 r_work: 0.2908 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3155 Z= 0.211 Angle : 0.534 6.241 4303 Z= 0.277 Chirality : 0.038 0.195 537 Planarity : 0.004 0.044 532 Dihedral : 6.562 58.494 459 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.49 % Allowed : 14.60 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.41), residues: 411 helix: 2.41 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -0.41 (0.76), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.006 0.001 PHE A 156 TYR 0.012 0.001 TYR A 299 ARG 0.003 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.327 Fit side-chains REVERT: A 334 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8114 (p) outliers start: 11 outliers final: 5 residues processed: 46 average time/residue: 1.2099 time to fit residues: 57.3517 Evaluate side-chains 42 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.111717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.075599 restraints weight = 5838.800| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.36 r_work: 0.2963 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3155 Z= 0.206 Angle : 0.539 6.904 4303 Z= 0.278 Chirality : 0.038 0.190 537 Planarity : 0.004 0.043 532 Dihedral : 6.565 58.921 459 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.49 % Allowed : 14.92 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.41), residues: 411 helix: 2.37 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.35 (0.79), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.006 0.001 PHE A 156 TYR 0.012 0.001 TYR A 299 ARG 0.002 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.345 Fit side-chains REVERT: A 334 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8374 (p) outliers start: 11 outliers final: 8 residues processed: 46 average time/residue: 1.4036 time to fit residues: 66.3719 Evaluate side-chains 44 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 416 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 0.0370 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.112851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.077315 restraints weight = 5708.617| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.42 r_work: 0.2952 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3155 Z= 0.177 Angle : 0.533 7.316 4303 Z= 0.274 Chirality : 0.037 0.185 537 Planarity : 0.004 0.042 532 Dihedral : 6.562 59.343 459 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.86 % Allowed : 15.87 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.41), residues: 411 helix: 2.42 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.34 (0.79), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.006 0.001 PHE A 156 TYR 0.008 0.001 TYR A 299 ARG 0.006 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.333 Fit side-chains REVERT: A 334 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8201 (p) outliers start: 9 outliers final: 5 residues processed: 43 average time/residue: 1.2668 time to fit residues: 56.0639 Evaluate side-chains 43 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 0.0970 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 11 optimal weight: 0.0570 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 overall best weight: 0.2296 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.115844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.080632 restraints weight = 5736.942| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.34 r_work: 0.3047 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3155 Z= 0.173 Angle : 0.546 7.102 4303 Z= 0.281 Chirality : 0.037 0.181 537 Planarity : 0.004 0.039 532 Dihedral : 6.574 59.813 459 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.54 % Allowed : 16.83 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.41), residues: 411 helix: 2.49 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.35 (0.78), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.006 0.001 PHE A 156 TYR 0.006 0.001 TYR A 299 ARG 0.006 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.325 Fit side-chains REVERT: A 334 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8398 (p) outliers start: 8 outliers final: 3 residues processed: 43 average time/residue: 1.2474 time to fit residues: 55.2760 Evaluate side-chains 43 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 416 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 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 = 0.3680 r_free = 0.3680 target = 0.113990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.078315 restraints weight = 5846.867| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.43 r_work: 0.2994 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3155 Z= 0.196 Angle : 0.564 7.253 4303 Z= 0.293 Chirality : 0.037 0.179 537 Planarity : 0.004 0.038 532 Dihedral : 6.577 60.179 459 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.54 % Allowed : 17.14 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.12 (0.41), residues: 411 helix: 2.44 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.30 (0.78), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.005 0.001 PHE A 156 TYR 0.009 0.001 TYR A 299 ARG 0.005 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.347 Fit side-chains REVERT: A 174 GLU cc_start: 0.7928 (mp0) cc_final: 0.7695 (mt-10) REVERT: A 334 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.8235 (p) outliers start: 8 outliers final: 3 residues processed: 46 average time/residue: 1.2668 time to fit residues: 59.9867 Evaluate side-chains 43 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 416 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 0.0060 chunk 12 optimal weight: 0.0000 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 0.4200 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.115279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.079937 restraints weight = 5641.298| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.31 r_work: 0.3039 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3155 Z= 0.185 Angle : 0.557 7.183 4303 Z= 0.289 Chirality : 0.037 0.177 537 Planarity : 0.004 0.036 532 Dihedral : 6.616 60.952 459 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.90 % Allowed : 19.37 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.41), residues: 411 helix: 2.48 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.18 (0.78), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.006 0.001 PHE A 156 TYR 0.008 0.001 TYR A 299 ARG 0.005 0.000 ARG A 287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.266 Fit side-chains REVERT: A 334 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8438 (p) outliers start: 6 outliers final: 2 residues processed: 40 average time/residue: 1.3146 time to fit residues: 54.0549 Evaluate side-chains 40 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 394 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.114224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.078336 restraints weight = 5909.288| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.45 r_work: 0.3001 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3155 Z= 0.195 Angle : 0.571 7.623 4303 Z= 0.298 Chirality : 0.037 0.173 537 Planarity : 0.004 0.035 532 Dihedral : 6.643 61.379 459 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.59 % Allowed : 20.32 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.16 (0.41), residues: 411 helix: 2.46 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.20 (0.80), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.006 0.001 PHE A 156 TYR 0.009 0.001 TYR A 299 ARG 0.006 0.001 ARG A 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3097.61 seconds wall clock time: 55 minutes 10.32 seconds (3310.32 seconds total)