Starting phenix.real_space_refine on Fri May 9 15:17:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jsx_36629/05_2025/8jsx_36629.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jsx_36629/05_2025/8jsx_36629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jsx_36629/05_2025/8jsx_36629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jsx_36629/05_2025/8jsx_36629.map" model { file = "/net/cci-nas-00/data/ceres_data/8jsx_36629/05_2025/8jsx_36629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jsx_36629/05_2025/8jsx_36629.cif" } resolution = 3.16 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= -0.002 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 1886 2.51 5 N 436 2.21 5 O 479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2828 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2816 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 23, 'TRANS': 354} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'E5E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.48, per 1000 atoms: 0.88 Number of scatterers: 2828 At special positions: 0 Unit cell: (57.8, 65.45, 72.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 479 8.00 N 436 7.00 C 1886 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: 0.71 Conformation dependent library (CDL) restraints added in 328.7 milliseconds 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 680 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 92.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 19 through 48 removed outlier: 3.622A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 129 through 157 removed outlier: 4.570A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.996A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 179 Processing helix chain 'A' and resid 181 through 211 Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.579A pdb=" N GLY A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 249 through 270 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 291 through 324 removed outlier: 3.866A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.721A pdb=" N LEU A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 3.505A pdb=" N LEU A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 381 through 414 removed outlier: 4.860A pdb=" N ALA A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 418 through 447 removed outlier: 3.613A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 435 " --> pdb=" O MET A 431 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.506A pdb=" N ARG A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) 238 hydrogen bonds defined for protein. 705 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: 0.72 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 500 1.33 - 1.45: 685 1.45 - 1.57: 1665 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 2896 Sorted by residual: bond pdb=" N VAL A 234 " pdb=" CA VAL A 234 " ideal model delta sigma weight residual 1.460 1.499 -0.040 1.21e-02 6.83e+03 1.08e+01 bond pdb=" N LEU A 315 " pdb=" CA LEU A 315 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.04e-02 9.25e+03 1.08e+01 bond pdb=" N ILE A 22 " pdb=" CA ILE A 22 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.21e-02 6.83e+03 1.04e+01 bond pdb=" N ILE A 162 " pdb=" CA ILE A 162 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.17e-02 7.31e+03 9.09e+00 bond pdb=" N LEU A 32 " pdb=" CA LEU A 32 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.23e-02 6.61e+03 8.46e+00 ... (remaining 2891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 3769 2.04 - 4.08: 152 4.08 - 6.12: 17 6.12 - 8.16: 3 8.16 - 10.21: 2 Bond angle restraints: 3943 Sorted by residual: angle pdb=" CA MET A 397 " pdb=" C MET A 397 " pdb=" O MET A 397 " ideal model delta sigma weight residual 120.55 116.34 4.21 1.06e+00 8.90e-01 1.58e+01 angle pdb=" CA LEU A 32 " pdb=" C LEU A 32 " pdb=" O LEU A 32 " ideal model delta sigma weight residual 120.42 116.34 4.08 1.06e+00 8.90e-01 1.48e+01 angle pdb=" CA GLY A 235 " pdb=" C GLY A 235 " pdb=" N PRO A 236 " ideal model delta sigma weight residual 116.69 122.91 -6.22 1.71e+00 3.42e-01 1.32e+01 angle pdb=" CA GLY A 235 " pdb=" C GLY A 235 " pdb=" O GLY A 235 " ideal model delta sigma weight residual 121.52 116.42 5.10 1.43e+00 4.89e-01 1.27e+01 angle pdb=" N PHE A 389 " pdb=" CA PHE A 389 " pdb=" C PHE A 389 " ideal model delta sigma weight residual 111.07 107.29 3.78 1.07e+00 8.73e-01 1.25e+01 ... (remaining 3938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 1500 17.47 - 34.94: 146 34.94 - 52.40: 41 52.40 - 69.87: 4 69.87 - 87.33: 3 Dihedral angle restraints: 1694 sinusoidal: 626 harmonic: 1068 Sorted by residual: dihedral pdb=" CB GLU A 244 " pdb=" CG GLU A 244 " pdb=" CD GLU A 244 " pdb=" OE1 GLU A 244 " ideal model delta sinusoidal sigma weight residual 0.00 85.83 -85.83 1 3.00e+01 1.11e-03 9.89e+00 dihedral pdb=" CG LYS A 290 " pdb=" CD LYS A 290 " pdb=" CE LYS A 290 " pdb=" NZ LYS A 290 " ideal model delta sinusoidal sigma weight residual 180.00 120.28 59.72 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG A 189 " pdb=" CB ARG A 189 " pdb=" CG ARG A 189 " pdb=" CD ARG A 189 " ideal model delta sinusoidal sigma weight residual 60.00 119.51 -59.51 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 336 0.046 - 0.093: 86 0.093 - 0.139: 37 0.139 - 0.185: 9 0.185 - 0.231: 6 Chirality restraints: 474 Sorted by residual: chirality pdb=" CA ILE A 25 " pdb=" N ILE A 25 " pdb=" C ILE A 25 " pdb=" CB ILE A 25 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA LEU A 228 " pdb=" N LEU A 228 " pdb=" C LEU A 228 " pdb=" CB LEU A 228 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA VAL A 391 " pdb=" N VAL A 391 " pdb=" C VAL A 391 " pdb=" CB VAL A 391 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 471 not shown) Planarity restraints: 483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 389 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C PHE A 389 " -0.036 2.00e-02 2.50e+03 pdb=" O PHE A 389 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY A 390 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 29 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" C ALA A 29 " 0.035 2.00e-02 2.50e+03 pdb=" O ALA A 29 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 30 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 391 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C VAL A 391 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL A 391 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 392 " -0.012 2.00e-02 2.50e+03 ... (remaining 480 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 1143 2.93 - 3.42: 3031 3.42 - 3.92: 4500 3.92 - 4.41: 4879 4.41 - 4.90: 8640 Nonbonded interactions: 22193 Sorted by model distance: nonbonded pdb=" O MET A 397 " pdb=" OG SER A 401 " model vdw 2.440 3.040 nonbonded pdb=" N ASN A 128 " pdb=" OD1 ASN A 128 " model vdw 2.450 3.120 nonbonded pdb=" O ALA A 29 " pdb=" OD1 ASP A 33 " model vdw 2.489 3.040 nonbonded pdb=" OH TYR A 433 " pdb=" OAD E5E A 501 " model vdw 2.490 3.040 nonbonded pdb=" O LEU A 186 " pdb=" OG SER A 190 " model vdw 2.554 3.040 ... (remaining 22188 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.300 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 : 0.005 0.050 2896 Z= 0.395 Angle : 0.843 10.206 3943 Z= 0.571 Chirality : 0.056 0.231 474 Planarity : 0.006 0.039 483 Dihedral : 15.280 87.334 1014 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.00 % Allowed : 20.67 % Favored : 78.33 % 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: 2.26 (0.46), residues: 374 helix: 2.28 (0.31), residues: 312 sheet: None (None), residues: 0 loop : -2.87 (0.68), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 PHE 0.019 0.002 PHE A 238 TYR 0.012 0.001 TYR A 422 ARG 0.004 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.12464 ( 238) hydrogen bonds : angle 6.06915 ( 705) covalent geometry : bond 0.00541 ( 2896) covalent geometry : angle 0.84263 ( 3943) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.301 Fit side-chains REVERT: A 306 MET cc_start: 0.8481 (ttt) cc_final: 0.7867 (ttt) outliers start: 3 outliers final: 2 residues processed: 42 average time/residue: 0.1708 time to fit residues: 8.6265 Evaluate side-chains 40 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 166 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.0980 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.144763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.127851 restraints weight = 3285.503| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.40 r_work: 0.3336 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2896 Z= 0.152 Angle : 0.637 10.256 3943 Z= 0.309 Chirality : 0.042 0.148 474 Planarity : 0.006 0.043 483 Dihedral : 5.003 37.465 406 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.00 % Allowed : 19.00 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.45), residues: 374 helix: 2.28 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -2.41 (0.74), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 328 HIS 0.003 0.001 HIS A 414 PHE 0.015 0.001 PHE A 238 TYR 0.016 0.001 TYR A 422 ARG 0.003 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.05682 ( 238) hydrogen bonds : angle 4.66066 ( 705) covalent geometry : bond 0.00334 ( 2896) covalent geometry : angle 0.63726 ( 3943) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.316 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 48 average time/residue: 0.1531 time to fit residues: 8.9823 Evaluate side-chains 41 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 416 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.0040 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.143229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.126157 restraints weight = 3289.705| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.40 r_work: 0.3314 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2896 Z= 0.154 Angle : 0.625 10.283 3943 Z= 0.303 Chirality : 0.042 0.143 474 Planarity : 0.006 0.047 483 Dihedral : 4.254 15.048 402 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.00 % Allowed : 20.67 % Favored : 77.33 % 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: 2.37 (0.45), residues: 374 helix: 2.26 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -2.33 (0.73), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 328 HIS 0.002 0.001 HIS A 414 PHE 0.016 0.001 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.002 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.05747 ( 238) hydrogen bonds : angle 4.59056 ( 705) covalent geometry : bond 0.00342 ( 2896) covalent geometry : angle 0.62492 ( 3943) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.269 Fit side-chains REVERT: A 334 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7526 (m-80) outliers start: 6 outliers final: 2 residues processed: 48 average time/residue: 0.1423 time to fit residues: 8.3564 Evaluate side-chains 41 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 416 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.0000 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.144378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.127339 restraints weight = 3332.831| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.42 r_work: 0.3329 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2896 Z= 0.142 Angle : 0.617 10.307 3943 Z= 0.298 Chirality : 0.042 0.158 474 Planarity : 0.006 0.046 483 Dihedral : 4.235 14.713 402 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.33 % Allowed : 20.67 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.45), residues: 374 helix: 2.33 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -2.27 (0.74), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 328 HIS 0.001 0.001 HIS A 414 PHE 0.016 0.001 PHE A 238 TYR 0.016 0.001 TYR A 422 ARG 0.002 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.05350 ( 238) hydrogen bonds : angle 4.48475 ( 705) covalent geometry : bond 0.00301 ( 2896) covalent geometry : angle 0.61745 ( 3943) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.278 Fit side-chains REVERT: A 334 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7458 (m-80) outliers start: 7 outliers final: 4 residues processed: 45 average time/residue: 0.1472 time to fit residues: 8.1341 Evaluate side-chains 43 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 416 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.141176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.123899 restraints weight = 3361.622| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.42 r_work: 0.2897 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2896 Z= 0.165 Angle : 0.642 10.337 3943 Z= 0.311 Chirality : 0.043 0.153 474 Planarity : 0.006 0.047 483 Dihedral : 4.275 15.571 402 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.33 % Allowed : 20.33 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.45), residues: 374 helix: 2.12 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.49 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 318 HIS 0.003 0.001 HIS A 414 PHE 0.016 0.001 PHE A 238 TYR 0.018 0.001 TYR A 422 ARG 0.002 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.06023 ( 238) hydrogen bonds : angle 4.56317 ( 705) covalent geometry : bond 0.00380 ( 2896) covalent geometry : angle 0.64244 ( 3943) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.311 Fit side-chains REVERT: A 329 GLN cc_start: 0.6949 (OUTLIER) cc_final: 0.5792 (mp10) REVERT: A 334 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7419 (m-80) outliers start: 7 outliers final: 4 residues processed: 44 average time/residue: 0.1532 time to fit residues: 8.2440 Evaluate side-chains 43 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 416 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 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 = 0.3613 r_free = 0.3613 target = 0.141908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.124611 restraints weight = 3359.579| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.42 r_work: 0.2910 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2896 Z= 0.156 Angle : 0.629 10.339 3943 Z= 0.306 Chirality : 0.042 0.151 474 Planarity : 0.006 0.047 483 Dihedral : 4.298 15.693 402 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.00 % Allowed : 21.00 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.45), residues: 374 helix: 2.07 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.50 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.015 0.001 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.001 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.05728 ( 238) hydrogen bonds : angle 4.58170 ( 705) covalent geometry : bond 0.00351 ( 2896) covalent geometry : angle 0.62920 ( 3943) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.271 Fit side-chains REVERT: A 329 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.5788 (mp10) REVERT: A 334 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7406 (m-80) outliers start: 6 outliers final: 4 residues processed: 42 average time/residue: 0.1618 time to fit residues: 8.2803 Evaluate side-chains 42 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 416 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 0.0000 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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 = 0.3306 r_free = 0.3306 target = 0.122490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.103953 restraints weight = 3483.912| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.38 r_work: 0.2948 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2896 Z= 0.149 Angle : 0.623 10.351 3943 Z= 0.302 Chirality : 0.042 0.150 474 Planarity : 0.006 0.045 483 Dihedral : 4.239 15.297 402 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.33 % Allowed : 21.00 % Favored : 76.67 % 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: 2.24 (0.45), residues: 374 helix: 2.13 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.51 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.015 0.001 PHE A 238 TYR 0.016 0.001 TYR A 422 ARG 0.002 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.05556 ( 238) hydrogen bonds : angle 4.54335 ( 705) covalent geometry : bond 0.00329 ( 2896) covalent geometry : angle 0.62313 ( 3943) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.322 Fit side-chains REVERT: A 329 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.5820 (mp10) REVERT: A 334 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7415 (m-80) outliers start: 7 outliers final: 4 residues processed: 44 average time/residue: 0.1667 time to fit residues: 8.9713 Evaluate side-chains 43 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 416 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3284 r_free = 0.3284 target = 0.121048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.102436 restraints weight = 3455.121| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.39 r_work: 0.2911 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2896 Z= 0.153 Angle : 0.655 10.769 3943 Z= 0.310 Chirality : 0.042 0.149 474 Planarity : 0.006 0.045 483 Dihedral : 4.254 15.427 402 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.33 % Allowed : 21.33 % Favored : 76.33 % 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: 2.19 (0.45), residues: 374 helix: 2.10 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.55 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.015 0.001 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.05675 ( 238) hydrogen bonds : angle 4.54361 ( 705) covalent geometry : bond 0.00343 ( 2896) covalent geometry : angle 0.65539 ( 3943) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.278 Fit side-chains REVERT: A 329 GLN cc_start: 0.6997 (OUTLIER) cc_final: 0.5797 (mp10) REVERT: A 334 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7426 (m-80) outliers start: 7 outliers final: 5 residues processed: 43 average time/residue: 0.1601 time to fit residues: 8.3580 Evaluate side-chains 44 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 416 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 4 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 0.0170 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.123295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.104930 restraints weight = 3432.666| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.38 r_work: 0.2935 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2896 Z= 0.143 Angle : 0.641 10.358 3943 Z= 0.303 Chirality : 0.041 0.148 474 Planarity : 0.006 0.044 483 Dihedral : 4.195 14.990 402 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.67 % Allowed : 21.00 % Favored : 76.33 % 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: 2.30 (0.46), residues: 374 helix: 2.18 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.52 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 451 HIS 0.002 0.001 HIS A 414 PHE 0.014 0.001 PHE A 238 TYR 0.015 0.001 TYR A 422 ARG 0.001 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.05329 ( 238) hydrogen bonds : angle 4.51101 ( 705) covalent geometry : bond 0.00306 ( 2896) covalent geometry : angle 0.64107 ( 3943) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.289 Fit side-chains REVERT: A 189 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7310 (tpt90) REVERT: A 329 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.5792 (mp10) REVERT: A 334 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7412 (m-80) outliers start: 8 outliers final: 5 residues processed: 44 average time/residue: 0.1759 time to fit residues: 9.2421 Evaluate side-chains 45 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 416 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.0060 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 8 optimal weight: 0.0870 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.0670 chunk 27 optimal weight: 0.4980 overall best weight: 0.2512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.128998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.110913 restraints weight = 3405.038| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.36 r_work: 0.2999 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2896 Z= 0.126 Angle : 0.620 10.278 3943 Z= 0.290 Chirality : 0.041 0.146 474 Planarity : 0.006 0.044 483 Dihedral : 4.077 13.976 402 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.00 % Allowed : 21.67 % Favored : 76.33 % 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: 2.65 (0.46), residues: 374 helix: 2.40 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.31 (0.74), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 328 HIS 0.001 0.000 HIS A 414 PHE 0.015 0.001 PHE A 348 TYR 0.011 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.04522 ( 238) hydrogen bonds : angle 4.40774 ( 705) covalent geometry : bond 0.00246 ( 2896) covalent geometry : angle 0.61968 ( 3943) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.278 Fit side-chains REVERT: A 189 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7247 (tpt90) REVERT: A 306 MET cc_start: 0.8424 (tpp) cc_final: 0.8141 (ttt) REVERT: A 329 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.5848 (mp10) REVERT: A 334 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7429 (m-80) outliers start: 6 outliers final: 3 residues processed: 46 average time/residue: 0.1795 time to fit residues: 9.8263 Evaluate side-chains 46 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.121159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.102965 restraints weight = 3409.614| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.37 r_work: 0.2935 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2896 Z= 0.157 Angle : 0.655 10.351 3943 Z= 0.310 Chirality : 0.042 0.147 474 Planarity : 0.006 0.044 483 Dihedral : 4.130 14.670 402 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.67 % Allowed : 22.33 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.46), residues: 374 helix: 2.16 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -2.45 (0.74), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.016 0.001 PHE A 238 TYR 0.018 0.001 TYR A 422 ARG 0.001 0.000 ARG A 413 Details of bonding type rmsd hydrogen bonds : bond 0.05649 ( 238) hydrogen bonds : angle 4.51300 ( 705) covalent geometry : bond 0.00360 ( 2896) covalent geometry : angle 0.65525 ( 3943) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1688.38 seconds wall clock time: 30 minutes 0.51 seconds (1800.51 seconds total)