Starting phenix.real_space_refine on Wed Mar 5 16:39:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jsx_36629/03_2025/8jsx_36629.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jsx_36629/03_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_36629/03_2025/8jsx_36629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jsx_36629/03_2025/8jsx_36629.map" model { file = "/net/cci-nas-00/data/ceres_data/8jsx_36629/03_2025/8jsx_36629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jsx_36629/03_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-5624/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: 3.00, per 1000 atoms: 1.06 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: 0.83 Conformation dependent library (CDL) restraints added in 450.6 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: 0.28 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: 0.76 Time building geometry restraints manager: 0.93 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.820 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.460 ------------------------------------------------------------------------------- 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= 0.347 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 *********************** 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 : 0.279 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: 0.1707 time to fit residues: 8.5902 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 : 0.285 ------------------------------------------------------------------------------- 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 = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.127850 restraints weight = 3285.503| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.39 r_work: 0.3338 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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= 0.218 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 *********************** 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 : 0.261 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 48 average time/residue: 0.1568 time to fit residues: 9.1682 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 : 0.297 ------------------------------------------------------------------------------- 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: 0.1980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 35 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 = 0.3635 r_free = 0.3635 target = 0.143552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.126479 restraints weight = 3285.435| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.41 r_work: 0.2938 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1073 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= 0.219 Angle : 0.623 10.280 3943 Z= 0.302 Chirality : 0.041 0.143 474 Planarity : 0.006 0.046 483 Dihedral : 4.246 14.928 402 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.29 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: 2.38 (0.45), residues: 374 helix: 2.27 (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 *********************** 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 : 0.298 Fit side-chains REVERT: A 334 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7406 (m-80) outliers start: 6 outliers final: 2 residues processed: 48 average time/residue: 0.1493 time to fit residues: 8.8003 Evaluate side-chains 40 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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: 0.9980 chunk 2 optimal weight: 0.0040 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.0010 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.144194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127246 restraints weight = 3329.523| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.41 r_work: 0.2956 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1215 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= 0.200 Angle : 0.619 10.301 3943 Z= 0.298 Chirality : 0.041 0.160 474 Planarity : 0.006 0.046 483 Dihedral : 4.234 14.731 402 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: 2.50 (0.45), residues: 374 helix: 2.36 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -2.22 (0.72), residues: 62 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 0.016 0.001 TYR A 422 ARG 0.002 0.000 ARG A 155 *********************** 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 44 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.307 Fit side-chains REVERT: A 334 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7336 (m-80) outliers start: 6 outliers final: 4 residues processed: 44 average time/residue: 0.1586 time to fit residues: 8.5090 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 : 0.307 ------------------------------------------------------------------------------- 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: 0.6980 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 0.0030 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.143984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126877 restraints weight = 3362.122| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.42 r_work: 0.2948 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1347 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= 0.204 Angle : 0.616 10.307 3943 Z= 0.297 Chirality : 0.041 0.153 474 Planarity : 0.006 0.046 483 Dihedral : 4.186 14.732 402 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.67 % Allowed : 20.00 % 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: 2.43 (0.45), residues: 374 helix: 2.25 (0.30), residues: 317 sheet: None (None), residues: 0 loop : -2.25 (0.74), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 328 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 155 *********************** 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 47 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.296 Fit side-chains REVERT: A 329 GLN cc_start: 0.6906 (OUTLIER) cc_final: 0.5777 (mp10) REVERT: A 334 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7343 (m-80) outliers start: 8 outliers final: 4 residues processed: 46 average time/residue: 0.1557 time to fit residues: 8.7404 Evaluate side-chains 44 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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: 0.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 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 = 0.3596 r_free = 0.3596 target = 0.140393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.122980 restraints weight = 3366.963| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.43 r_work: 0.2886 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1599 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= 0.253 Angle : 0.646 10.373 3943 Z= 0.314 Chirality : 0.042 0.152 474 Planarity : 0.006 0.047 483 Dihedral : 4.318 15.898 402 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.77 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: 2.18 (0.45), residues: 374 helix: 2.07 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.38 (0.74), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.003 0.001 HIS A 414 PHE 0.016 0.001 PHE A 238 TYR 0.019 0.001 TYR A 422 ARG 0.002 0.000 ARG A 217 *********************** 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 43 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.300 Fit side-chains REVERT: A 329 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.5827 (mp10) REVERT: A 334 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7411 (m-80) outliers start: 7 outliers final: 4 residues processed: 43 average time/residue: 0.1632 time to fit residues: 8.5236 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 : 0.268 ------------------------------------------------------------------------------- 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: 0.0040 chunk 14 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 = 0.3292 r_free = 0.3292 target = 0.121585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.102890 restraints weight = 3489.450| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.40 r_work: 0.2925 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1615 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= 0.215 Angle : 0.647 10.348 3943 Z= 0.307 Chirality : 0.042 0.150 474 Planarity : 0.006 0.046 483 Dihedral : 4.271 15.482 402 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % 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: 2.28 (0.45), residues: 374 helix: 2.13 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.29 (0.75), 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 0.001 0.000 ARG A 155 *********************** 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 44 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.304 Fit side-chains REVERT: A 329 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.5789 (mp10) REVERT: A 334 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7383 (m-80) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 0.1621 time to fit residues: 8.6102 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 : 0.322 ------------------------------------------------------------------------------- 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: 0.0010 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.122432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.104037 restraints weight = 3452.274| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.36 r_work: 0.2938 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1652 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= 0.200 Angle : 0.637 10.346 3943 Z= 0.302 Chirality : 0.041 0.150 474 Planarity : 0.006 0.044 483 Dihedral : 4.213 14.945 402 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.00 % Allowed : 21.33 % 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: 2.38 (0.46), residues: 374 helix: 2.19 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.25 (0.76), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 328 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 217 *********************** 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 42 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.285 Fit side-chains REVERT: A 329 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.5821 (mp10) REVERT: A 334 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7399 (m-80) outliers start: 6 outliers final: 4 residues processed: 41 average time/residue: 0.1662 time to fit residues: 8.2710 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 : 0.305 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 4 optimal weight: 0.5980 chunk 35 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 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: 0.7980 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 = 0.3288 r_free = 0.3288 target = 0.121362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.103013 restraints weight = 3440.702| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.35 r_work: 0.2923 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1722 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= 0.221 Angle : 0.648 10.362 3943 Z= 0.307 Chirality : 0.042 0.148 474 Planarity : 0.006 0.044 483 Dihedral : 4.214 15.230 402 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.77 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: 2.29 (0.45), residues: 374 helix: 2.13 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.25 (0.76), 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 *********************** 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 44 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.308 Fit side-chains REVERT: A 329 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.5820 (mp10) REVERT: A 334 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7411 (m-80) outliers start: 7 outliers final: 5 residues processed: 43 average time/residue: 0.1607 time to fit residues: 8.4042 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 : 0.300 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.0670 chunk 27 optimal weight: 2.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.124225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.105801 restraints weight = 3414.139| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.38 r_work: 0.2945 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2896 Z= 0.188 Angle : 0.632 10.342 3943 Z= 0.300 Chirality : 0.041 0.148 474 Planarity : 0.006 0.044 483 Dihedral : 4.178 14.682 402 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.67 % Allowed : 20.67 % 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: 2.48 (0.46), residues: 374 helix: 2.23 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -2.06 (0.78), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.014 0.001 PHE A 238 TYR 0.014 0.001 TYR A 422 ARG 0.001 0.000 ARG A 155 ********************** 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 46 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.306 Fit side-chains REVERT: A 189 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7199 (tpt90) REVERT: A 329 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.5799 (mp10) REVERT: A 334 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7390 (m-80) outliers start: 8 outliers final: 5 residues processed: 45 average time/residue: 0.1792 time to fit residues: 9.5619 Evaluate side-chains 46 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 19 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 1 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 = 0.3266 r_free = 0.3266 target = 0.119930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.101389 restraints weight = 3393.570| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.37 r_work: 0.2906 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1806 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= 0.234 Angle : 0.655 10.396 3943 Z= 0.312 Chirality : 0.042 0.147 474 Planarity : 0.006 0.044 483 Dihedral : 4.225 15.310 402 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.67 % Allowed : 20.67 % 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: 2.26 (0.45), residues: 374 helix: 2.11 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.27 (0.76), 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 0.016 0.001 PHE A 238 TYR 0.018 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1781.02 seconds wall clock time: 31 minutes 20.08 seconds (1880.08 seconds total)