Starting phenix.real_space_refine on Fri Dec 27 08:12:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hiz_34830/12_2024/8hiz_34830_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hiz_34830/12_2024/8hiz_34830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hiz_34830/12_2024/8hiz_34830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hiz_34830/12_2024/8hiz_34830.map" model { file = "/net/cci-nas-00/data/ceres_data/8hiz_34830/12_2024/8hiz_34830_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hiz_34830/12_2024/8hiz_34830_neut.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2083 2.51 5 N 553 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3274 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3226 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.32, per 1000 atoms: 1.01 Number of scatterers: 3274 At special positions: 0 Unit cell: (67.048, 73.95, 71.978, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 3 15.00 O 621 8.00 N 553 7.00 C 2083 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: 0.85 Conformation dependent library (CDL) restraints added in 416.0 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 54.1% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 Processing helix chain 'A' and resid 24 through 33 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.701A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.914A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 206 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 302 through 307 removed outlier: 4.410A pdb=" N ASP A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 344 through 361 removed outlier: 4.497A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.533A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279 removed outlier: 6.473A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 243 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 187 hydrogen bonds defined for protein. 546 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: 0.99 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1063 1.35 - 1.46: 766 1.46 - 1.58: 1490 1.58 - 1.70: 5 1.70 - 1.81: 27 Bond restraints: 3351 Sorted by residual: bond pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 1.736 1.614 0.122 2.00e-02 2.50e+03 3.69e+01 bond pdb=" N LYS A 213 " pdb=" CA LYS A 213 " ideal model delta sigma weight residual 1.453 1.486 -0.032 1.27e-02 6.20e+03 6.40e+00 bond pdb=" C1D NAP A 501 " pdb=" O4D NAP A 501 " ideal model delta sigma weight residual 1.375 1.425 -0.050 2.00e-02 2.50e+03 6.13e+00 bond pdb=" C5D NAP A 501 " pdb=" O5D NAP A 501 " ideal model delta sigma weight residual 1.403 1.449 -0.046 2.00e-02 2.50e+03 5.38e+00 bond pdb=" O5D NAP A 501 " pdb=" PN NAP A 501 " ideal model delta sigma weight residual 1.649 1.604 0.045 2.00e-02 2.50e+03 5.04e+00 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 4376 1.53 - 3.07: 142 3.07 - 4.60: 36 4.60 - 6.14: 3 6.14 - 7.67: 4 Bond angle restraints: 4561 Sorted by residual: angle pdb=" O GLY A 212 " pdb=" C GLY A 212 " pdb=" N LYS A 213 " ideal model delta sigma weight residual 122.41 126.80 -4.39 1.25e+00 6.40e-01 1.23e+01 angle pdb=" CA GLY A 212 " pdb=" C GLY A 212 " pdb=" N LYS A 213 " ideal model delta sigma weight residual 118.42 114.17 4.25 1.26e+00 6.30e-01 1.14e+01 angle pdb=" C VAL A 146 " pdb=" N TYR A 147 " pdb=" CA TYR A 147 " ideal model delta sigma weight residual 123.05 127.62 -4.57 1.57e+00 4.06e-01 8.47e+00 angle pdb=" CA GLY A 254 " pdb=" C GLY A 254 " pdb=" N LEU A 255 " ideal model delta sigma weight residual 114.23 116.53 -2.30 8.80e-01 1.29e+00 6.83e+00 angle pdb=" C2B NAP A 501 " pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 117.19 109.52 7.67 3.00e+00 1.11e-01 6.54e+00 ... (remaining 4556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 1787 17.73 - 35.45: 180 35.45 - 53.18: 41 53.18 - 70.90: 17 70.90 - 88.63: 7 Dihedral angle restraints: 2032 sinusoidal: 843 harmonic: 1189 Sorted by residual: dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 164.56 15.44 0 5.00e+00 4.00e-02 9.53e+00 dihedral pdb=" CA LYS A 213 " pdb=" CB LYS A 213 " pdb=" CG LYS A 213 " pdb=" CD LYS A 213 " ideal model delta sinusoidal sigma weight residual -60.00 -114.74 54.74 3 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" CB LYS A 167 " pdb=" CG LYS A 167 " pdb=" CD LYS A 167 " pdb=" CE LYS A 167 " ideal model delta sinusoidal sigma weight residual 60.00 114.59 -54.59 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 2029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 288 0.026 - 0.053: 120 0.053 - 0.079: 46 0.079 - 0.105: 33 0.105 - 0.131: 14 Chirality restraints: 501 Sorted by residual: chirality pdb=" CA ILE A 37 " pdb=" N ILE A 37 " pdb=" C ILE A 37 " pdb=" CB ILE A 37 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE A 108 " pdb=" N ILE A 108 " pdb=" C ILE A 108 " pdb=" CB ILE A 108 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA PRO A 150 " pdb=" N PRO A 150 " pdb=" C PRO A 150 " pdb=" CB PRO A 150 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.62e-01 ... (remaining 498 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAP A 501 " -0.002 2.00e-02 2.50e+03 3.33e-02 2.22e+01 pdb=" C2N NAP A 501 " 0.023 2.00e-02 2.50e+03 pdb=" C3N NAP A 501 " 0.015 2.00e-02 2.50e+03 pdb=" C4N NAP A 501 " 0.064 2.00e-02 2.50e+03 pdb=" C5N NAP A 501 " -0.043 2.00e-02 2.50e+03 pdb=" C6N NAP A 501 " -0.014 2.00e-02 2.50e+03 pdb=" C7N NAP A 501 " -0.045 2.00e-02 2.50e+03 pdb=" N1N NAP A 501 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO A 142 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 212 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C GLY A 212 " 0.028 2.00e-02 2.50e+03 pdb=" O GLY A 212 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS A 213 " -0.010 2.00e-02 2.50e+03 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1056 2.84 - 3.35: 3369 3.35 - 3.87: 5827 3.87 - 4.38: 6598 4.38 - 4.90: 11179 Nonbonded interactions: 28029 Sorted by model distance: nonbonded pdb=" ND1 HIS A 388 " pdb=" O ILE A 393 " model vdw 2.324 3.120 nonbonded pdb=" OD2 ASP A 244 " pdb=" OG SER A 269 " model vdw 2.329 3.040 nonbonded pdb=" O PHE A 171 " pdb=" NZ LYS A 177 " model vdw 2.356 3.120 nonbonded pdb=" OE1 GLU A 383 " pdb=" NH2 ARG A 406 " model vdw 2.357 3.120 nonbonded pdb=" N ILE A 4 " pdb=" OG SER A 81 " model vdw 2.379 3.120 ... (remaining 28024 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: 0.700 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.590 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 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 : 0.004 0.122 3351 Z= 0.282 Angle : 0.703 7.671 4561 Z= 0.393 Chirality : 0.042 0.131 501 Planarity : 0.005 0.048 579 Dihedral : 16.641 88.630 1274 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.30 % Allowed : 0.00 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.44), residues: 414 helix: 2.04 (0.36), residues: 211 sheet: -0.07 (0.66), residues: 70 loop : 0.02 (0.59), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 355 HIS 0.001 0.000 HIS A 388 PHE 0.012 0.001 PHE A 381 TYR 0.018 0.001 TYR A 250 ARG 0.007 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.396 Fit side-chains REVERT: A 30 TRP cc_start: 0.8868 (t-100) cc_final: 0.8645 (t-100) REVERT: A 218 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7876 (tp40) REVERT: A 332 GLU cc_start: 0.7669 (pp20) cc_final: 0.7407 (pp20) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.1599 time to fit residues: 13.6293 Evaluate side-chains 57 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3351 Z= 0.194 Angle : 0.533 8.495 4561 Z= 0.269 Chirality : 0.043 0.129 501 Planarity : 0.004 0.043 579 Dihedral : 11.017 65.150 517 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.61 % Allowed : 6.67 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.43), residues: 414 helix: 2.13 (0.36), residues: 211 sheet: -0.11 (0.67), residues: 72 loop : -0.27 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 355 HIS 0.006 0.001 HIS A 267 PHE 0.009 0.001 PHE A 381 TYR 0.012 0.001 TYR A 160 ARG 0.005 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.388 Fit side-chains REVERT: A 218 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7747 (tp40) REVERT: A 251 ASN cc_start: 0.8248 (t0) cc_final: 0.8027 (t0) outliers start: 2 outliers final: 0 residues processed: 64 average time/residue: 0.1626 time to fit residues: 12.7726 Evaluate side-chains 54 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 3351 Z= 0.360 Angle : 0.594 5.404 4561 Z= 0.307 Chirality : 0.044 0.143 501 Planarity : 0.005 0.043 579 Dihedral : 9.887 67.415 517 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.52 % Allowed : 9.09 % Favored : 89.39 % 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: 0.98 (0.43), residues: 414 helix: 1.65 (0.36), residues: 211 sheet: -0.36 (0.64), residues: 73 loop : -0.26 (0.58), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 355 HIS 0.006 0.001 HIS A 267 PHE 0.011 0.002 PHE A 381 TYR 0.013 0.002 TYR A 363 ARG 0.005 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.373 Fit side-chains REVERT: A 281 ASN cc_start: 0.7387 (m110) cc_final: 0.6986 (m-40) REVERT: A 332 GLU cc_start: 0.7774 (pp20) cc_final: 0.7460 (pp20) outliers start: 5 outliers final: 3 residues processed: 65 average time/residue: 0.1732 time to fit residues: 13.6538 Evaluate side-chains 54 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3351 Z= 0.205 Angle : 0.544 9.652 4561 Z= 0.276 Chirality : 0.043 0.131 501 Planarity : 0.004 0.047 579 Dihedral : 8.894 56.598 517 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.61 % Allowed : 13.33 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.43), residues: 414 helix: 1.72 (0.35), residues: 212 sheet: -0.36 (0.67), residues: 71 loop : -0.28 (0.58), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 355 HIS 0.006 0.001 HIS A 267 PHE 0.015 0.001 PHE A 381 TYR 0.008 0.001 TYR A 160 ARG 0.004 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.352 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 0.1683 time to fit residues: 12.3178 Evaluate side-chains 53 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 3351 Z= 0.214 Angle : 0.549 6.742 4561 Z= 0.275 Chirality : 0.042 0.136 501 Planarity : 0.004 0.048 579 Dihedral : 8.378 51.216 517 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.91 % Allowed : 15.45 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.43), residues: 414 helix: 1.77 (0.36), residues: 212 sheet: -0.17 (0.67), residues: 69 loop : -0.39 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 355 HIS 0.006 0.001 HIS A 267 PHE 0.013 0.001 PHE A 381 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.347 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 58 average time/residue: 0.1697 time to fit residues: 12.0913 Evaluate side-chains 54 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 215 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 3351 Z= 0.313 Angle : 0.610 10.938 4561 Z= 0.305 Chirality : 0.043 0.145 501 Planarity : 0.005 0.046 579 Dihedral : 8.165 53.690 517 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.21 % Allowed : 14.55 % Favored : 84.24 % 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: 0.90 (0.43), residues: 414 helix: 1.59 (0.36), residues: 211 sheet: -0.15 (0.70), residues: 61 loop : -0.48 (0.56), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 355 HIS 0.006 0.001 HIS A 267 PHE 0.013 0.001 PHE A 381 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.355 Fit side-chains REVERT: A 396 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7541 (ttm-80) outliers start: 4 outliers final: 3 residues processed: 64 average time/residue: 0.1788 time to fit residues: 13.7809 Evaluate side-chains 58 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 3351 Z= 0.268 Angle : 0.593 8.904 4561 Z= 0.296 Chirality : 0.043 0.144 501 Planarity : 0.004 0.047 579 Dihedral : 7.821 48.682 517 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.52 % Allowed : 16.67 % Favored : 81.82 % 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: 0.84 (0.43), residues: 414 helix: 1.53 (0.36), residues: 211 sheet: -0.17 (0.70), residues: 61 loop : -0.49 (0.56), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 355 HIS 0.007 0.001 HIS A 267 PHE 0.014 0.001 PHE A 381 TYR 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.405 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 60 average time/residue: 0.1589 time to fit residues: 11.8037 Evaluate side-chains 59 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.0030 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 28 optimal weight: 8.9990 overall best weight: 0.4768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3351 Z= 0.183 Angle : 0.585 10.884 4561 Z= 0.286 Chirality : 0.042 0.138 501 Planarity : 0.004 0.049 579 Dihedral : 7.422 52.551 517 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.30 % Allowed : 18.18 % Favored : 81.52 % 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: 0.96 (0.43), residues: 414 helix: 1.67 (0.36), residues: 212 sheet: -0.34 (0.70), residues: 63 loop : -0.41 (0.56), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 355 HIS 0.014 0.002 HIS A 267 PHE 0.012 0.001 PHE A 381 TYR 0.005 0.001 TYR A 363 ARG 0.002 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.366 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 64 average time/residue: 0.1520 time to fit residues: 12.1934 Evaluate side-chains 60 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 0.2980 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN A 267 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3351 Z= 0.207 Angle : 0.593 9.814 4561 Z= 0.293 Chirality : 0.042 0.138 501 Planarity : 0.004 0.049 579 Dihedral : 7.282 56.118 517 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.91 % Allowed : 18.48 % Favored : 80.61 % 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: 0.94 (0.43), residues: 414 helix: 1.65 (0.35), residues: 212 sheet: -0.11 (0.71), residues: 61 loop : -0.54 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 355 HIS 0.008 0.002 HIS A 267 PHE 0.011 0.001 PHE A 381 TYR 0.025 0.002 TYR A 160 ARG 0.001 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.413 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 57 average time/residue: 0.1698 time to fit residues: 11.9489 Evaluate side-chains 56 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 267 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 0.0770 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.0170 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN A 267 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3351 Z= 0.184 Angle : 0.589 9.550 4561 Z= 0.293 Chirality : 0.042 0.134 501 Planarity : 0.004 0.050 579 Dihedral : 7.188 57.689 517 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.61 % Allowed : 19.09 % Favored : 80.30 % 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: 0.94 (0.43), residues: 414 helix: 1.68 (0.36), residues: 212 sheet: -0.10 (0.72), residues: 60 loop : -0.60 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 355 HIS 0.007 0.001 HIS A 267 PHE 0.012 0.001 PHE A 381 TYR 0.025 0.001 TYR A 160 ARG 0.002 0.000 ARG A 331 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.383 Fit side-chains REVERT: A 299 GLU cc_start: 0.8159 (mp0) cc_final: 0.7768 (mp0) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.1625 time to fit residues: 12.4407 Evaluate side-chains 61 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 267 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 40.0000 chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN A 267 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.160017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.134807 restraints weight = 6044.408| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.53 r_work: 0.3651 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3351 Z= 0.226 Angle : 0.611 9.296 4561 Z= 0.305 Chirality : 0.043 0.138 501 Planarity : 0.004 0.048 579 Dihedral : 7.210 59.658 517 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.91 % Allowed : 19.09 % Favored : 80.00 % 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: 0.85 (0.43), residues: 414 helix: 1.58 (0.35), residues: 212 sheet: -0.13 (0.72), residues: 61 loop : -0.60 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 355 HIS 0.003 0.001 HIS A 267 PHE 0.012 0.001 PHE A 381 TYR 0.024 0.002 TYR A 160 ARG 0.003 0.000 ARG A 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1190.89 seconds wall clock time: 22 minutes 23.74 seconds (1343.74 seconds total)