Starting phenix.real_space_refine on Fri Aug 22 13:00:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jsx_36629/08_2025/8jsx_36629.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jsx_36629/08_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_36629/08_2025/8jsx_36629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jsx_36629/08_2025/8jsx_36629.map" model { file = "/net/cci-nas-00/data/ceres_data/8jsx_36629/08_2025/8jsx_36629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jsx_36629/08_2025/8jsx_36629.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 0.86, per 1000 atoms: 0.30 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: 0.27 Conformation dependent library (CDL) restraints added in 105.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.05 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: 0.33 Time building geometry restraints manager: 0.35 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: 2.370 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.540 Find NCS groups from input model: 0.010 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.980 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 155 TYR 0.012 0.001 TYR A 422 PHE 0.019 0.002 PHE A 238 TRP 0.009 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 2896) covalent geometry : angle 0.84263 ( 3943) hydrogen bonds : bond 0.12464 ( 238) hydrogen bonds : angle 6.06915 ( 705) *********************** 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 : 0.061 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: 0.0554 time to fit residues: 2.8163 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 : 0.060 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.0010 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.145509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.128500 restraints weight = 3330.750| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.41 r_work: 0.3345 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2896 Z= 0.148 Angle : 0.633 10.266 3943 Z= 0.306 Chirality : 0.042 0.144 474 Planarity : 0.006 0.042 483 Dihedral : 4.980 37.343 406 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.33 % Allowed : 19.00 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.45), residues: 374 helix: 2.33 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -2.32 (0.73), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 155 TYR 0.016 0.001 TYR A 422 PHE 0.015 0.001 PHE A 348 TRP 0.003 0.001 TRP A 328 HIS 0.003 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 2896) covalent geometry : angle 0.63333 ( 3943) hydrogen bonds : bond 0.05530 ( 238) hydrogen bonds : angle 4.63405 ( 705) *********************** 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 49 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.105 Fit side-chains REVERT: A 334 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7560 (m-80) outliers start: 7 outliers final: 3 residues processed: 49 average time/residue: 0.0630 time to fit residues: 3.7096 Evaluate side-chains 43 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.141871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124521 restraints weight = 3430.076| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.44 r_work: 0.2909 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1189 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= 0.165 Angle : 0.639 10.301 3943 Z= 0.310 Chirality : 0.042 0.142 474 Planarity : 0.006 0.046 483 Dihedral : 4.279 15.536 402 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.00 % Allowed : 20.33 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.45), residues: 374 helix: 2.20 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -2.37 (0.72), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 155 TYR 0.018 0.001 TYR A 422 PHE 0.015 0.001 PHE A 238 TRP 0.002 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 2896) covalent geometry : angle 0.63854 ( 3943) hydrogen bonds : bond 0.06074 ( 238) hydrogen bonds : angle 4.61834 ( 705) *********************** 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 46 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.114 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 46 average time/residue: 0.0674 time to fit residues: 3.7448 Evaluate side-chains 39 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 0.0980 chunk 11 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.143183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.126214 restraints weight = 3393.146| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.42 r_work: 0.2932 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1305 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= 0.148 Angle : 0.627 10.326 3943 Z= 0.302 Chirality : 0.042 0.159 474 Planarity : 0.006 0.043 483 Dihedral : 4.272 15.331 402 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.45), residues: 374 helix: 2.26 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -2.31 (0.74), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 155 TYR 0.016 0.001 TYR A 422 PHE 0.015 0.001 PHE A 238 TRP 0.002 0.001 TRP A 328 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 2896) covalent geometry : angle 0.62684 ( 3943) hydrogen bonds : bond 0.05595 ( 238) hydrogen bonds : angle 4.52853 ( 705) *********************** 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 : 0.104 Fit side-chains REVERT: A 334 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7379 (m-80) outliers start: 7 outliers final: 4 residues processed: 44 average time/residue: 0.0709 time to fit residues: 3.7620 Evaluate side-chains 42 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.084 ------------------------------------------------------------------------------- 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 15 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.141367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.124238 restraints weight = 3334.461| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.40 r_work: 0.2931 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1460 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= 0.161 Angle : 0.638 10.339 3943 Z= 0.308 Chirality : 0.042 0.154 474 Planarity : 0.006 0.042 483 Dihedral : 4.277 15.661 402 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.45), residues: 374 helix: 2.10 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.48 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 155 TYR 0.017 0.001 TYR A 422 PHE 0.016 0.001 PHE A 238 TRP 0.003 0.001 TRP A 318 HIS 0.003 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 2896) covalent geometry : angle 0.63752 ( 3943) hydrogen bonds : bond 0.05903 ( 238) hydrogen bonds : angle 4.55258 ( 705) *********************** 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 42 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.064 Fit side-chains REVERT: A 329 GLN cc_start: 0.6943 (OUTLIER) cc_final: 0.6052 (mt0) REVERT: A 334 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7417 (m-80) outliers start: 6 outliers final: 4 residues processed: 42 average time/residue: 0.0654 time to fit residues: 3.2984 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 : 0.065 ------------------------------------------------------------------------------- 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 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 0.0010 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 = 0.141781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.124366 restraints weight = 3403.222| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.44 r_work: 0.2904 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1572 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= 0.155 Angle : 0.630 10.348 3943 Z= 0.305 Chirality : 0.042 0.151 474 Planarity : 0.006 0.042 483 Dihedral : 4.270 15.615 402 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.77 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.45), residues: 374 helix: 2.10 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.52 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 155 TYR 0.017 0.001 TYR A 422 PHE 0.015 0.001 PHE A 238 TRP 0.003 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 2896) covalent geometry : angle 0.63042 ( 3943) hydrogen bonds : bond 0.05717 ( 238) hydrogen bonds : angle 4.58434 ( 705) *********************** 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 : 0.101 Fit side-chains REVERT: A 329 GLN cc_start: 0.6955 (OUTLIER) cc_final: 0.6048 (mt0) REVERT: A 334 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7365 (m-80) outliers start: 6 outliers final: 4 residues processed: 42 average time/residue: 0.0554 time to fit residues: 2.8289 Evaluate side-chains 41 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.061 ------------------------------------------------------------------------------- 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 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.141514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.124206 restraints weight = 3363.854| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.42 r_work: 0.2925 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1662 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= 0.155 Angle : 0.631 10.366 3943 Z= 0.306 Chirality : 0.042 0.151 474 Planarity : 0.006 0.041 483 Dihedral : 4.255 15.499 402 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.00 % Allowed : 22.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.45), residues: 374 helix: 2.08 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.57 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 155 TYR 0.017 0.001 TYR A 422 PHE 0.015 0.001 PHE A 238 TRP 0.003 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 2896) covalent geometry : angle 0.63119 ( 3943) hydrogen bonds : bond 0.05745 ( 238) hydrogen bonds : angle 4.57749 ( 705) *********************** 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 43 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.094 Fit side-chains REVERT: A 329 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.5829 (mp10) REVERT: A 334 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7386 (m-80) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 0.0618 time to fit residues: 3.2191 Evaluate side-chains 41 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.100 ------------------------------------------------------------------------------- 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 8 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 0.0970 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3331 r_free = 0.3331 target = 0.124096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.105496 restraints weight = 3450.222| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.41 r_work: 0.2922 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1699 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= 0.146 Angle : 0.627 10.368 3943 Z= 0.304 Chirality : 0.042 0.149 474 Planarity : 0.006 0.040 483 Dihedral : 4.231 15.201 402 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.33 % Allowed : 22.00 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.46), residues: 374 helix: 2.15 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.55 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 155 TYR 0.015 0.001 TYR A 422 PHE 0.014 0.001 PHE A 238 TRP 0.003 0.001 TRP A 328 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 2896) covalent geometry : angle 0.62724 ( 3943) hydrogen bonds : bond 0.05435 ( 238) hydrogen bonds : angle 4.52522 ( 705) *********************** 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: 7 poor density : 35 time to evaluate : 0.071 Fit side-chains REVERT: A 306 MET cc_start: 0.8465 (tpp) cc_final: 0.8227 (ttt) REVERT: A 329 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.5752 (mp10) REVERT: A 334 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7402 (m-80) outliers start: 7 outliers final: 4 residues processed: 41 average time/residue: 0.0678 time to fit residues: 3.2996 Evaluate side-chains 41 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.089 ------------------------------------------------------------------------------- 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 15 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.119186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.100218 restraints weight = 3507.220| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.43 r_work: 0.2884 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 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= 0.167 Angle : 0.675 10.584 3943 Z= 0.321 Chirality : 0.043 0.149 474 Planarity : 0.006 0.040 483 Dihedral : 4.282 15.737 402 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.00 % Allowed : 22.67 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.45), residues: 374 helix: 2.05 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.63 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.018 0.001 TYR A 422 PHE 0.016 0.001 PHE A 238 TRP 0.004 0.001 TRP A 318 HIS 0.003 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 2896) covalent geometry : angle 0.67543 ( 3943) hydrogen bonds : bond 0.06036 ( 238) hydrogen bonds : angle 4.57777 ( 705) *********************** 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: 6 poor density : 38 time to evaluate : 0.102 Fit side-chains REVERT: A 329 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.5813 (mp10) REVERT: A 334 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7412 (m-80) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 0.0677 time to fit residues: 3.5296 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 : 0.106 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.3295 r_free = 0.3295 target = 0.122235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.103516 restraints weight = 3422.981| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.40 r_work: 0.2937 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1772 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= 0.141 Angle : 0.644 10.337 3943 Z= 0.305 Chirality : 0.042 0.148 474 Planarity : 0.006 0.040 483 Dihedral : 4.210 14.863 402 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.00 % Allowed : 22.33 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.46), residues: 374 helix: 2.20 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.58 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.014 0.001 TYR A 422 PHE 0.014 0.001 PHE A 348 TRP 0.003 0.001 TRP A 328 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 2896) covalent geometry : angle 0.64432 ( 3943) hydrogen bonds : bond 0.05193 ( 238) hydrogen bonds : angle 4.47763 ( 705) ********************** 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 42 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.106 Fit side-chains REVERT: A 329 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6064 (mt0) REVERT: A 334 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7378 (m-80) outliers start: 6 outliers final: 4 residues processed: 41 average time/residue: 0.0685 time to fit residues: 3.3769 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 : 0.062 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.0870 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.122786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.104231 restraints weight = 3424.355| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.38 r_work: 0.2938 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1798 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= 0.143 Angle : 0.646 10.471 3943 Z= 0.305 Chirality : 0.042 0.147 474 Planarity : 0.006 0.040 483 Dihedral : 4.164 14.646 402 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.33 % Allowed : 22.33 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.46), residues: 374 helix: 2.20 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -2.61 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.015 0.001 TYR A 422 PHE 0.014 0.001 PHE A 238 TRP 0.003 0.001 TRP A 328 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 2896) covalent geometry : angle 0.64619 ( 3943) hydrogen bonds : bond 0.05283 ( 238) hydrogen bonds : angle 4.47201 ( 705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 790.11 seconds wall clock time: 14 minutes 14.80 seconds (854.80 seconds total)