Starting phenix.real_space_refine on Mon Jun 24 17:02:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y65_38966/06_2024/8y65_38966_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y65_38966/06_2024/8y65_38966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y65_38966/06_2024/8y65_38966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y65_38966/06_2024/8y65_38966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y65_38966/06_2024/8y65_38966_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y65_38966/06_2024/8y65_38966_updated.pdb" } resolution = 3.51 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= 0.007 sd= 0.171 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 13 5.16 5 C 2355 2.51 5 N 574 2.21 5 O 623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 3565 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3553 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 442} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'URC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.46, per 1000 atoms: 0.69 Number of scatterers: 3565 At special positions: 0 Unit cell: (84.5383, 62.5803, 69.1677, 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 13 16.00 O 623 8.00 N 574 7.00 C 2355 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 - 3.50 Amino acid : False - 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: 1.38 Conformation dependent library (CDL) restraints added in 650.7 milliseconds 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 848 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 0 sheets defined 79.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 55 through 75 removed outlier: 4.372A pdb=" N PHE A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 97 Processing helix chain 'A' and resid 103 through 133 removed outlier: 4.794A pdb=" N PHE A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N MET A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 156 Processing helix chain 'A' and resid 158 through 161 No H-bonds generated for 'chain 'A' and resid 158 through 161' Processing helix chain 'A' and resid 164 through 192 Proline residue: A 186 - end of helix removed outlier: 3.848A pdb=" N GLU A 191 " --> pdb=" O MET A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 218 removed outlier: 3.816A pdb=" N ARG A 198 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLY A 199 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 200 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 204 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 205 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE A 208 " --> pdb=" O THR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 237 through 251 Proline residue: A 241 - end of helix removed outlier: 4.802A pdb=" N LEU A 249 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 283 through 298 Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 311 through 330 removed outlier: 5.608A pdb=" N TRP A 315 " --> pdb=" O TYR A 312 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 329 " --> pdb=" O CYS A 326 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS A 330 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 353 through 378 removed outlier: 4.064A pdb=" N LEU A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU A 376 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 403 Processing helix chain 'A' and resid 411 through 427 removed outlier: 3.979A pdb=" N ILE A 416 " --> pdb=" O TYR A 413 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS A 427 " --> pdb=" O ALA A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 Proline residue: A 434 - end of helix removed outlier: 4.708A pdb=" N GLY A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 475 Proline residue: A 470 - end of helix Processing helix chain 'A' and resid 481 through 498 Processing helix chain 'A' and resid 507 through 517 244 hydrogen bonds defined for protein. 585 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: 0.96 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1101 1.34 - 1.46: 872 1.46 - 1.58: 1664 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3655 Sorted by residual: bond pdb=" C4 URC A 601 " pdb=" C5 URC A 601 " ideal model delta sigma weight residual 1.358 1.470 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C6 URC A 601 " pdb=" N1 URC A 601 " ideal model delta sigma weight residual 1.398 1.317 0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C8 URC A 601 " pdb=" N9 URC A 601 " ideal model delta sigma weight residual 1.396 1.316 0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" N ILE A 335 " pdb=" CA ILE A 335 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.10e+01 bond pdb=" C2 URC A 601 " pdb=" N3 URC A 601 " ideal model delta sigma weight residual 1.376 1.311 0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 3650 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.91: 111 106.91 - 114.25: 2130 114.25 - 121.59: 2076 121.59 - 128.92: 643 128.92 - 136.26: 29 Bond angle restraints: 4989 Sorted by residual: angle pdb=" N7 URC A 601 " pdb=" C8 URC A 601 " pdb=" N9 URC A 601 " ideal model delta sigma weight residual 104.73 118.77 -14.04 3.00e+00 1.11e-01 2.19e+01 angle pdb=" N ILE A 436 " pdb=" CA ILE A 436 " pdb=" C ILE A 436 " ideal model delta sigma weight residual 112.96 108.33 4.63 1.00e+00 1.00e+00 2.15e+01 angle pdb=" CA ILE A 335 " pdb=" C ILE A 335 " pdb=" N TRP A 336 " ideal model delta sigma weight residual 118.13 123.44 -5.31 1.37e+00 5.33e-01 1.50e+01 angle pdb=" N1 URC A 601 " pdb=" C2 URC A 601 " pdb=" N3 URC A 601 " ideal model delta sigma weight residual 114.62 124.69 -10.07 3.00e+00 1.11e-01 1.13e+01 angle pdb=" N ILE A 335 " pdb=" CA ILE A 335 " pdb=" C ILE A 335 " ideal model delta sigma weight residual 113.00 108.67 4.33 1.30e+00 5.92e-01 1.11e+01 ... (remaining 4984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 1911 17.37 - 34.73: 166 34.73 - 52.10: 26 52.10 - 69.46: 4 69.46 - 86.83: 4 Dihedral angle restraints: 2111 sinusoidal: 781 harmonic: 1330 Sorted by residual: dihedral pdb=" CA GLY A 331 " pdb=" C GLY A 331 " pdb=" N LEU A 332 " pdb=" CA LEU A 332 " ideal model delta harmonic sigma weight residual 180.00 163.26 16.74 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CB GLU A 223 " pdb=" CG GLU A 223 " pdb=" CD GLU A 223 " pdb=" OE1 GLU A 223 " ideal model delta sinusoidal sigma weight residual 0.00 -86.83 86.83 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU A 287 " pdb=" CG GLU A 287 " pdb=" CD GLU A 287 " pdb=" OE1 GLU A 287 " ideal model delta sinusoidal sigma weight residual 0.00 86.24 -86.24 1 3.00e+01 1.11e-03 9.97e+00 ... (remaining 2108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 425 0.039 - 0.079: 125 0.079 - 0.118: 37 0.118 - 0.158: 3 0.158 - 0.197: 2 Chirality restraints: 592 Sorted by residual: chirality pdb=" CB ILE A 335 " pdb=" CA ILE A 335 " pdb=" CG1 ILE A 335 " pdb=" CG2 ILE A 335 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CB ILE A 197 " pdb=" CA ILE A 197 " pdb=" CG1 ILE A 197 " pdb=" CG2 ILE A 197 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA ILE A 348 " pdb=" N ILE A 348 " pdb=" C ILE A 348 " pdb=" CB ILE A 348 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 589 not shown) Planarity restraints: 618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 381 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A 382 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 255 " 0.038 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO A 256 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 256 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 256 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 335 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C ILE A 335 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE A 335 " 0.014 2.00e-02 2.50e+03 pdb=" N TRP A 336 " 0.014 2.00e-02 2.50e+03 ... (remaining 615 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 675 2.76 - 3.30: 3598 3.30 - 3.83: 6150 3.83 - 4.37: 6438 4.37 - 4.90: 11456 Nonbonded interactions: 28317 Sorted by model distance: nonbonded pdb=" NH2 ARG A 96 " pdb=" O GLY A 162 " model vdw 2.231 2.520 nonbonded pdb=" NE2 GLN A 328 " pdb=" OD1 ASN A 458 " model vdw 2.281 2.520 nonbonded pdb=" OE1 GLN A 328 " pdb=" ND2 ASN A 333 " model vdw 2.335 2.520 nonbonded pdb=" NZ LYS A 195 " pdb=" OE2 GLU A 288 " model vdw 2.343 2.520 nonbonded pdb=" O GLY A 136 " pdb=" OG1 THR A 140 " model vdw 2.353 2.440 ... (remaining 28312 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 group one per residue 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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.550 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.840 Find NCS groups from input model: 0.100 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5316 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 0.112 3655 Z= 0.311 Angle : 0.734 14.038 4989 Z= 0.355 Chirality : 0.041 0.197 592 Planarity : 0.005 0.063 618 Dihedral : 13.646 86.828 1263 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.27 % Allowed : 0.27 % Favored : 99.47 % 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: 1.81 (0.42), residues: 465 helix: 1.61 (0.29), residues: 363 sheet: None (None), residues: 0 loop : -0.14 (0.69), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 93 HIS 0.002 0.000 HIS A 377 PHE 0.012 0.001 PHE A 208 TYR 0.007 0.001 TYR A 327 ARG 0.003 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.373 Fit side-chains REVERT: A 400 ILE cc_start: 0.7317 (tp) cc_final: 0.6686 (tt) outliers start: 1 outliers final: 1 residues processed: 29 average time/residue: 0.1528 time to fit residues: 5.9253 Evaluate side-chains 23 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.0070 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 0.0040 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.2810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5337 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3655 Z= 0.165 Angle : 0.571 8.140 4989 Z= 0.295 Chirality : 0.040 0.138 592 Planarity : 0.006 0.043 618 Dihedral : 4.100 20.206 500 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.27 % Allowed : 5.32 % Favored : 94.41 % 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: 1.43 (0.42), residues: 465 helix: 1.38 (0.29), residues: 357 sheet: None (None), residues: 0 loop : -0.31 (0.69), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 377 PHE 0.018 0.001 PHE A 276 TYR 0.004 0.001 TYR A 507 ARG 0.004 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.373 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 27 average time/residue: 0.1073 time to fit residues: 4.2778 Evaluate side-chains 24 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.0570 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 0.0770 chunk 33 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5399 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3655 Z= 0.171 Angle : 0.561 8.110 4989 Z= 0.282 Chirality : 0.040 0.134 592 Planarity : 0.005 0.035 618 Dihedral : 3.976 17.016 498 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.53 % Allowed : 8.51 % Favored : 90.96 % 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: 1.29 (0.42), residues: 465 helix: 1.30 (0.29), residues: 360 sheet: None (None), residues: 0 loop : -0.52 (0.69), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 231 HIS 0.002 0.000 HIS A 377 PHE 0.013 0.001 PHE A 276 TYR 0.005 0.001 TYR A 233 ARG 0.004 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 0.376 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 27 average time/residue: 0.0822 time to fit residues: 3.6678 Evaluate side-chains 26 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 44 optimal weight: 0.0670 chunk 39 optimal weight: 0.0870 chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5404 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3655 Z= 0.164 Angle : 0.555 8.541 4989 Z= 0.276 Chirality : 0.040 0.143 592 Planarity : 0.005 0.031 618 Dihedral : 3.967 16.378 498 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.06 % Allowed : 9.57 % Favored : 89.36 % 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: 1.30 (0.42), residues: 465 helix: 1.30 (0.29), residues: 360 sheet: None (None), residues: 0 loop : -0.47 (0.68), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.002 0.000 HIS A 377 PHE 0.007 0.001 PHE A 276 TYR 0.004 0.001 TYR A 507 ARG 0.003 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 22 time to evaluate : 0.372 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 25 average time/residue: 0.0846 time to fit residues: 3.4577 Evaluate side-chains 25 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.0570 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 39 optimal weight: 0.0010 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 overall best weight: 0.4304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5421 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3655 Z= 0.160 Angle : 0.536 6.538 4989 Z= 0.267 Chirality : 0.040 0.139 592 Planarity : 0.004 0.031 618 Dihedral : 3.933 15.920 498 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.33 % Allowed : 11.70 % Favored : 86.97 % 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: 1.16 (0.42), residues: 465 helix: 1.19 (0.29), residues: 366 sheet: None (None), residues: 0 loop : -0.61 (0.70), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 231 HIS 0.002 0.000 HIS A 377 PHE 0.005 0.001 PHE A 395 TYR 0.004 0.001 TYR A 258 ARG 0.004 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.379 Fit side-chains REVERT: A 262 GLU cc_start: -0.0974 (OUTLIER) cc_final: -0.1892 (tp30) outliers start: 5 outliers final: 4 residues processed: 27 average time/residue: 0.1232 time to fit residues: 4.7944 Evaluate side-chains 27 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 chunk 20 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5456 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3655 Z= 0.180 Angle : 0.566 7.723 4989 Z= 0.283 Chirality : 0.040 0.139 592 Planarity : 0.004 0.031 618 Dihedral : 3.985 15.524 498 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.39 % Allowed : 11.97 % Favored : 85.64 % 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: 1.26 (0.41), residues: 465 helix: 1.28 (0.29), residues: 354 sheet: None (None), residues: 0 loop : -0.44 (0.63), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.002 0.001 HIS A 377 PHE 0.005 0.001 PHE A 514 TYR 0.005 0.001 TYR A 233 ARG 0.002 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 21 time to evaluate : 0.363 Fit side-chains REVERT: A 262 GLU cc_start: -0.1037 (OUTLIER) cc_final: -0.1687 (tp30) REVERT: A 427 CYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7408 (t) outliers start: 9 outliers final: 5 residues processed: 29 average time/residue: 0.1119 time to fit residues: 4.7446 Evaluate side-chains 27 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 20 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 427 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 44 optimal weight: 0.0060 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 0.0000 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5463 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3655 Z= 0.169 Angle : 0.551 8.595 4989 Z= 0.275 Chirality : 0.040 0.151 592 Planarity : 0.004 0.031 618 Dihedral : 3.979 15.278 498 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.13 % Allowed : 11.97 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.41), residues: 465 helix: 1.20 (0.29), residues: 360 sheet: None (None), residues: 0 loop : -0.35 (0.65), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.002 0.000 HIS A 377 PHE 0.010 0.001 PHE A 276 TYR 0.004 0.001 TYR A 258 ARG 0.001 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 22 time to evaluate : 0.304 Fit side-chains REVERT: A 262 GLU cc_start: -0.1011 (OUTLIER) cc_final: -0.1685 (tp30) REVERT: A 427 CYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7395 (t) outliers start: 8 outliers final: 6 residues processed: 28 average time/residue: 0.1218 time to fit residues: 4.8415 Evaluate side-chains 29 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 21 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 427 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 38 optimal weight: 0.0370 chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5482 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3655 Z= 0.186 Angle : 0.563 9.154 4989 Z= 0.282 Chirality : 0.040 0.156 592 Planarity : 0.004 0.031 618 Dihedral : 3.999 15.148 498 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.39 % Allowed : 12.23 % Favored : 85.37 % 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: 1.11 (0.41), residues: 465 helix: 1.13 (0.29), residues: 359 sheet: None (None), residues: 0 loop : -0.40 (0.65), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.002 0.000 HIS A 377 PHE 0.005 0.001 PHE A 514 TYR 0.009 0.001 TYR A 73 ARG 0.002 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 22 time to evaluate : 0.389 Fit side-chains REVERT: A 262 GLU cc_start: -0.1015 (OUTLIER) cc_final: -0.1693 (tp30) REVERT: A 427 CYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7395 (t) outliers start: 9 outliers final: 7 residues processed: 29 average time/residue: 0.0872 time to fit residues: 4.0162 Evaluate side-chains 31 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 22 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 427 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5501 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3655 Z= 0.187 Angle : 0.564 9.734 4989 Z= 0.282 Chirality : 0.040 0.160 592 Planarity : 0.004 0.031 618 Dihedral : 4.043 15.079 498 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.39 % Allowed : 12.23 % Favored : 85.37 % 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: 1.01 (0.41), residues: 465 helix: 1.07 (0.28), residues: 360 sheet: None (None), residues: 0 loop : -0.46 (0.65), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.002 0.000 HIS A 377 PHE 0.005 0.001 PHE A 442 TYR 0.012 0.001 TYR A 73 ARG 0.002 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 26 time to evaluate : 0.396 Fit side-chains REVERT: A 262 GLU cc_start: -0.1037 (OUTLIER) cc_final: -0.1741 (tp30) REVERT: A 427 CYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7392 (t) outliers start: 9 outliers final: 6 residues processed: 32 average time/residue: 0.1351 time to fit residues: 5.9047 Evaluate side-chains 32 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 24 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 427 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 0.0040 chunk 42 optimal weight: 0.0570 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 overall best weight: 0.3110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5444 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3655 Z= 0.160 Angle : 0.548 9.410 4989 Z= 0.274 Chirality : 0.040 0.178 592 Planarity : 0.004 0.031 618 Dihedral : 3.962 14.914 498 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.86 % Allowed : 13.03 % Favored : 85.11 % 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: 1.14 (0.41), residues: 465 helix: 1.15 (0.29), residues: 360 sheet: None (None), residues: 0 loop : -0.38 (0.66), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 377 PHE 0.005 0.001 PHE A 442 TYR 0.009 0.001 TYR A 73 ARG 0.001 0.000 ARG A 381 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 26 time to evaluate : 0.359 Fit side-chains REVERT: A 262 GLU cc_start: -0.1044 (OUTLIER) cc_final: -0.1740 (tp30) REVERT: A 427 CYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7418 (t) outliers start: 7 outliers final: 5 residues processed: 31 average time/residue: 0.1137 time to fit residues: 5.0421 Evaluate side-chains 33 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 26 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 427 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 0.0010 chunk 15 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.276389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.253476 restraints weight = 3941.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.257997 restraints weight = 2392.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.261021 restraints weight = 1630.336| |-----------------------------------------------------------------------------| r_work (final): 0.4672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5505 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3655 Z= 0.174 Angle : 0.552 9.246 4989 Z= 0.277 Chirality : 0.040 0.168 592 Planarity : 0.004 0.031 618 Dihedral : 3.984 14.986 498 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.86 % Allowed : 12.50 % Favored : 85.64 % 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: 1.05 (0.41), residues: 465 helix: 1.10 (0.28), residues: 360 sheet: None (None), residues: 0 loop : -0.47 (0.65), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 231 HIS 0.002 0.000 HIS A 377 PHE 0.005 0.001 PHE A 514 TYR 0.012 0.001 TYR A 73 ARG 0.002 0.000 ARG A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1049.53 seconds wall clock time: 19 minutes 44.19 seconds (1184.19 seconds total)