Starting phenix.real_space_refine on Tue Feb 13 22:04:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0l_15787/02_2024/8b0l_15787_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0l_15787/02_2024/8b0l_15787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0l_15787/02_2024/8b0l_15787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0l_15787/02_2024/8b0l_15787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0l_15787/02_2024/8b0l_15787_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0l_15787/02_2024/8b0l_15787_updated.pdb" } resolution = 3.13 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= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3861 atoms to isotropic. 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 1 5.49 5 S 14 5.16 5 C 2658 2.51 5 N 662 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4033 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4033 Unusual residues: {'PTY': 1} Classifications: {'peptide': 510, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 36, 'TRANS': 473, None: 1} Not linked: pdbres="ARG A 510 " pdbres="PTY A 601 " Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 2.74, per 1000 atoms: 0.68 Number of scatterers: 4033 At special positions: 0 Unit cell: (60.298, 80.948, 85.904, 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 1 15.00 O 698 8.00 N 662 7.00 C 2658 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: 1.56 Conformation dependent library (CDL) restraints added in 734.5 milliseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 4 sheets defined 51.0% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 10 through 27 removed outlier: 3.536A pdb=" N LEU A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA A 27 " --> pdb=" O CYS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 47 removed outlier: 3.683A pdb=" N ILE A 38 " --> pdb=" O TRP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 69 Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.659A pdb=" N PHE A 82 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 115 removed outlier: 4.195A pdb=" N TYR A 104 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 127 through 144 removed outlier: 6.315A pdb=" N LEU A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N THR A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 157 removed outlier: 4.329A pdb=" N ASP A 157 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.488A pdb=" N GLY A 162 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 189 Processing helix chain 'A' and resid 193 through 210 Proline residue: A 205 - end of helix removed outlier: 4.162A pdb=" N LEU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR A 210 " --> pdb=" O PHE A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 256 removed outlier: 3.792A pdb=" N ASN A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 278 through 291 Processing helix chain 'A' and resid 351 through 354 No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 393 through 399 Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 421 through 436 Processing helix chain 'A' and resid 482 through 486 Processing helix chain 'A' and resid 489 through 509 Processing sheet with id= A, first strand: chain 'A' and resid 222 through 227 Processing sheet with id= B, first strand: chain 'A' and resid 294 through 296 Processing sheet with id= C, first strand: chain 'A' and resid 299 through 304 Processing sheet with id= D, first strand: chain 'A' and resid 375 through 377 removed outlier: 6.994A pdb=" N TYR A 406 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALA A 385 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 408 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N THR A 409 " --> pdb=" O PRO A 439 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU A 441 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N SER A 411 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER A 443 " --> pdb=" O SER A 411 " (cutoff:3.500A) 183 hydrogen bonds defined for protein. 495 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: 1.03 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 616 1.31 - 1.43: 1146 1.43 - 1.56: 2355 1.56 - 1.68: 3 1.68 - 1.81: 26 Bond restraints: 4146 Sorted by residual: bond pdb=" C8 PTY A 601 " pdb=" O7 PTY A 601 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C30 PTY A 601 " pdb=" O4 PTY A 601 " ideal model delta sigma weight residual 1.331 1.397 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" CA PHE A 344 " pdb=" CB PHE A 344 " ideal model delta sigma weight residual 1.529 1.570 -0.041 1.54e-02 4.22e+03 7.15e+00 bond pdb=" C6 PTY A 601 " pdb=" O7 PTY A 601 " ideal model delta sigma weight residual 1.432 1.396 0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" C1 PTY A 601 " pdb=" O4 PTY A 601 " ideal model delta sigma weight residual 1.427 1.397 0.030 2.00e-02 2.50e+03 2.27e+00 ... (remaining 4141 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.24: 191 107.24 - 113.93: 2326 113.93 - 120.61: 1668 120.61 - 127.30: 1400 127.30 - 133.98: 69 Bond angle restraints: 5654 Sorted by residual: angle pdb=" O11 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O14 PTY A 601 " ideal model delta sigma weight residual 92.90 109.53 -16.63 3.00e+00 1.11e-01 3.07e+01 angle pdb=" O12 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O13 PTY A 601 " ideal model delta sigma weight residual 119.61 109.32 10.29 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C11 PTY A 601 " pdb=" C8 PTY A 601 " pdb=" O7 PTY A 601 " ideal model delta sigma weight residual 111.29 120.05 -8.76 3.00e+00 1.11e-01 8.52e+00 angle pdb=" C31 PTY A 601 " pdb=" C30 PTY A 601 " pdb=" O4 PTY A 601 " ideal model delta sigma weight residual 111.62 120.14 -8.52 3.00e+00 1.11e-01 8.07e+00 angle pdb=" N THR A 315 " pdb=" CA THR A 315 " pdb=" C THR A 315 " ideal model delta sigma weight residual 109.85 112.97 -3.12 1.58e+00 4.01e-01 3.89e+00 ... (remaining 5649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.06: 2341 20.06 - 40.13: 83 40.13 - 60.19: 12 60.19 - 80.25: 0 80.25 - 100.31: 4 Dihedral angle restraints: 2440 sinusoidal: 974 harmonic: 1466 Sorted by residual: dihedral pdb=" CA GLY A 71 " pdb=" C GLY A 71 " pdb=" N ILE A 72 " pdb=" CA ILE A 72 " ideal model delta harmonic sigma weight residual 180.00 160.99 19.01 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" C3 PTY A 601 " pdb=" O11 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O12 PTY A 601 " ideal model delta sinusoidal sigma weight residual -59.77 40.54 -100.31 1 3.00e+01 1.11e-03 1.26e+01 dihedral pdb=" CA ASN A 314 " pdb=" C ASN A 314 " pdb=" N THR A 315 " pdb=" CA THR A 315 " ideal model delta harmonic sigma weight residual -180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 2437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 334 0.024 - 0.048: 168 0.048 - 0.072: 64 0.072 - 0.095: 44 0.095 - 0.119: 25 Chirality restraints: 635 Sorted by residual: chirality pdb=" CA ILE A 270 " pdb=" N ILE A 270 " pdb=" C ILE A 270 " pdb=" CB ILE A 270 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 chirality pdb=" CA ILE A 231 " pdb=" N ILE A 231 " pdb=" C ILE A 231 " pdb=" CB ILE A 231 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.55e-01 chirality pdb=" CA ILE A 316 " pdb=" N ILE A 316 " pdb=" C ILE A 316 " pdb=" CB ILE A 316 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 632 not shown) Planarity restraints: 708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 421 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 422 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 422 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 422 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 34 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A 35 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 35 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 35 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 204 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A 205 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 205 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 205 " -0.017 5.00e-02 4.00e+02 ... (remaining 705 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1002 2.80 - 3.32: 4035 3.32 - 3.85: 6910 3.85 - 4.37: 8109 4.37 - 4.90: 14216 Nonbonded interactions: 34272 Sorted by model distance: nonbonded pdb=" O ALA A 98 " pdb=" OG SER A 102 " model vdw 2.270 2.440 nonbonded pdb=" O PHE A 151 " pdb=" OG SER A 154 " model vdw 2.278 2.440 nonbonded pdb=" O SER A 261 " pdb=" OG SER A 294 " model vdw 2.283 2.440 nonbonded pdb=" OD2 ASP A 331 " pdb=" OG SER A 376 " model vdw 2.297 2.440 nonbonded pdb=" ND2 ASN A 336 " pdb=" O GLY A 368 " model vdw 2.317 2.520 ... (remaining 34267 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 3.070 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.120 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 : 0.003 0.067 4146 Z= 0.205 Angle : 0.665 16.632 5654 Z= 0.290 Chirality : 0.041 0.119 635 Planarity : 0.004 0.034 708 Dihedral : 10.816 100.314 1500 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.48 % Allowed : 3.12 % Favored : 96.39 % 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: 1.39 (0.41), residues: 508 helix: 2.21 (0.34), residues: 253 sheet: -0.26 (0.69), residues: 69 loop : -0.37 (0.51), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 492 HIS 0.001 0.001 HIS A 425 PHE 0.008 0.001 PHE A 174 TYR 0.008 0.001 TYR A 104 ARG 0.003 0.000 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.408 Fit side-chains REVERT: A 33 VAL cc_start: 0.8740 (t) cc_final: 0.8329 (p) REVERT: A 230 ASP cc_start: 0.8294 (t0) cc_final: 0.7954 (t0) REVERT: A 468 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7045 (tm-30) REVERT: A 488 ASN cc_start: 0.8490 (m-40) cc_final: 0.8288 (m110) outliers start: 2 outliers final: 0 residues processed: 91 average time/residue: 0.1645 time to fit residues: 18.6291 Evaluate side-chains 54 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN A 241 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4146 Z= 0.214 Angle : 0.545 7.303 5654 Z= 0.263 Chirality : 0.042 0.126 635 Planarity : 0.005 0.038 708 Dihedral : 9.360 85.890 594 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.44 % Allowed : 8.65 % Favored : 89.90 % 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: 1.23 (0.40), residues: 508 helix: 2.11 (0.33), residues: 251 sheet: -0.58 (0.66), residues: 69 loop : -0.36 (0.50), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 74 HIS 0.001 0.001 HIS A 425 PHE 0.025 0.001 PHE A 465 TYR 0.013 0.001 TYR A 104 ARG 0.005 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.405 Fit side-chains REVERT: A 230 ASP cc_start: 0.8294 (t0) cc_final: 0.7990 (t0) REVERT: A 341 PHE cc_start: 0.8816 (m-10) cc_final: 0.8592 (m-10) REVERT: A 468 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7015 (tm-30) outliers start: 6 outliers final: 4 residues processed: 59 average time/residue: 0.1279 time to fit residues: 10.1276 Evaluate side-chains 54 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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: 0.8107 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4146 Z= 0.210 Angle : 0.521 5.766 5654 Z= 0.252 Chirality : 0.042 0.128 635 Planarity : 0.004 0.033 708 Dihedral : 8.206 71.128 594 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.44 % Allowed : 11.06 % Favored : 87.50 % 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 (0.40), residues: 508 helix: 1.92 (0.33), residues: 257 sheet: -0.68 (0.65), residues: 69 loop : -0.33 (0.51), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 74 HIS 0.001 0.000 HIS A 337 PHE 0.017 0.001 PHE A 465 TYR 0.009 0.001 TYR A 104 ARG 0.003 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.568 Fit side-chains REVERT: A 230 ASP cc_start: 0.8134 (t0) cc_final: 0.7900 (t0) REVERT: A 468 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7015 (tm-30) outliers start: 6 outliers final: 4 residues processed: 56 average time/residue: 0.1323 time to fit residues: 10.0161 Evaluate side-chains 56 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 444 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.8104 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4146 Z= 0.194 Angle : 0.512 5.447 5654 Z= 0.246 Chirality : 0.041 0.126 635 Planarity : 0.004 0.038 708 Dihedral : 7.431 59.047 594 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.44 % Allowed : 12.26 % Favored : 86.30 % 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: 1.19 (0.40), residues: 508 helix: 2.01 (0.33), residues: 254 sheet: -0.68 (0.64), residues: 69 loop : -0.27 (0.50), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 74 HIS 0.001 0.000 HIS A 337 PHE 0.016 0.001 PHE A 465 TYR 0.014 0.001 TYR A 104 ARG 0.003 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.486 Fit side-chains REVERT: A 230 ASP cc_start: 0.8133 (t0) cc_final: 0.7892 (t0) REVERT: A 341 PHE cc_start: 0.8785 (m-10) cc_final: 0.8538 (m-10) REVERT: A 468 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7008 (tm-30) outliers start: 6 outliers final: 3 residues processed: 58 average time/residue: 0.1411 time to fit residues: 10.7711 Evaluate side-chains 56 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.0570 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- 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: 0.8110 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4146 Z= 0.202 Angle : 0.520 5.310 5654 Z= 0.251 Chirality : 0.042 0.128 635 Planarity : 0.004 0.038 708 Dihedral : 7.031 56.964 594 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.68 % Allowed : 12.26 % 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: 1.17 (0.39), residues: 508 helix: 1.98 (0.33), residues: 254 sheet: -0.68 (0.64), residues: 69 loop : -0.26 (0.50), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 213 HIS 0.001 0.000 HIS A 337 PHE 0.012 0.001 PHE A 82 TYR 0.010 0.001 TYR A 104 ARG 0.004 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.430 Fit side-chains REVERT: A 230 ASP cc_start: 0.8154 (t0) cc_final: 0.7884 (t0) REVERT: A 461 MET cc_start: 0.9029 (ttt) cc_final: 0.8783 (ttt) REVERT: A 468 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7016 (tm-30) outliers start: 7 outliers final: 6 residues processed: 58 average time/residue: 0.1381 time to fit residues: 10.6241 Evaluate side-chains 57 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 493 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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: 0.8154 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4146 Z= 0.322 Angle : 0.585 9.786 5654 Z= 0.282 Chirality : 0.044 0.138 635 Planarity : 0.004 0.040 708 Dihedral : 6.978 58.322 594 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.40 % Allowed : 11.78 % Favored : 85.82 % 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: 0.94 (0.39), residues: 508 helix: 1.80 (0.33), residues: 253 sheet: -0.90 (0.62), residues: 69 loop : -0.34 (0.51), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 213 HIS 0.001 0.001 HIS A 337 PHE 0.013 0.001 PHE A 82 TYR 0.017 0.001 TYR A 104 ARG 0.004 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.442 Fit side-chains REVERT: A 230 ASP cc_start: 0.8202 (t0) cc_final: 0.7950 (t0) REVERT: A 341 PHE cc_start: 0.8764 (m-10) cc_final: 0.8528 (m-10) REVERT: A 468 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7071 (tm-30) outliers start: 10 outliers final: 6 residues processed: 57 average time/residue: 0.1245 time to fit residues: 9.7529 Evaluate side-chains 55 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 493 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 0.0470 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4146 Z= 0.156 Angle : 0.536 12.145 5654 Z= 0.254 Chirality : 0.042 0.127 635 Planarity : 0.004 0.039 708 Dihedral : 6.656 56.517 594 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.68 % Allowed : 13.46 % Favored : 84.86 % 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: 1.07 (0.39), residues: 508 helix: 1.95 (0.33), residues: 254 sheet: -0.78 (0.62), residues: 69 loop : -0.37 (0.50), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 74 HIS 0.000 0.000 HIS A 337 PHE 0.012 0.001 PHE A 82 TYR 0.011 0.001 TYR A 104 ARG 0.004 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.400 Fit side-chains REVERT: A 85 MET cc_start: 0.7598 (mmm) cc_final: 0.7221 (mmp) REVERT: A 230 ASP cc_start: 0.8165 (t0) cc_final: 0.7904 (t0) REVERT: A 341 PHE cc_start: 0.8743 (m-10) cc_final: 0.8494 (m-10) REVERT: A 468 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7012 (tm-30) outliers start: 7 outliers final: 6 residues processed: 56 average time/residue: 0.1293 time to fit residues: 9.6677 Evaluate side-chains 59 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 42 optimal weight: 0.0270 chunk 45 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 0.0770 chunk 14 optimal weight: 2.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4146 Z= 0.143 Angle : 0.521 10.683 5654 Z= 0.249 Chirality : 0.042 0.127 635 Planarity : 0.004 0.041 708 Dihedral : 6.416 53.277 594 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.68 % Allowed : 13.22 % Favored : 85.10 % 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 (0.39), residues: 508 helix: 2.01 (0.33), residues: 254 sheet: -0.69 (0.62), residues: 69 loop : -0.34 (0.50), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 74 HIS 0.000 0.000 HIS A 425 PHE 0.009 0.001 PHE A 465 TYR 0.010 0.001 TYR A 104 ARG 0.004 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.440 Fit side-chains REVERT: A 85 MET cc_start: 0.7611 (mmm) cc_final: 0.7105 (mtp) REVERT: A 230 ASP cc_start: 0.8114 (t0) cc_final: 0.7865 (t0) REVERT: A 341 PHE cc_start: 0.8751 (m-10) cc_final: 0.8504 (m-10) REVERT: A 468 GLU cc_start: 0.7873 (mm-30) cc_final: 0.6979 (tm-30) outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 0.1234 time to fit residues: 9.7531 Evaluate side-chains 54 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4146 Z= 0.162 Angle : 0.526 9.886 5654 Z= 0.252 Chirality : 0.042 0.127 635 Planarity : 0.004 0.040 708 Dihedral : 6.228 47.905 594 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.20 % Allowed : 14.18 % Favored : 84.62 % 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: 1.18 (0.39), residues: 508 helix: 2.04 (0.33), residues: 254 sheet: -0.58 (0.62), residues: 69 loop : -0.40 (0.50), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 415 HIS 0.000 0.000 HIS A 337 PHE 0.008 0.001 PHE A 174 TYR 0.013 0.001 TYR A 104 ARG 0.002 0.000 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.482 Fit side-chains REVERT: A 85 MET cc_start: 0.7560 (mmm) cc_final: 0.7134 (mtt) REVERT: A 230 ASP cc_start: 0.8131 (t0) cc_final: 0.7890 (t0) REVERT: A 341 PHE cc_start: 0.8741 (m-10) cc_final: 0.8493 (m-10) REVERT: A 461 MET cc_start: 0.8972 (ttt) cc_final: 0.8633 (ttt) REVERT: A 468 GLU cc_start: 0.7852 (mm-30) cc_final: 0.6964 (tm-30) outliers start: 5 outliers final: 5 residues processed: 53 average time/residue: 0.1174 time to fit residues: 8.6344 Evaluate side-chains 56 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8100 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4146 Z= 0.172 Angle : 0.524 9.628 5654 Z= 0.250 Chirality : 0.042 0.130 635 Planarity : 0.004 0.041 708 Dihedral : 6.118 46.706 594 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.20 % Allowed : 14.90 % Favored : 83.89 % 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: 1.09 (0.39), residues: 508 helix: 2.09 (0.33), residues: 253 sheet: -0.77 (0.65), residues: 59 loop : -0.59 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 213 HIS 0.001 0.000 HIS A 337 PHE 0.008 0.001 PHE A 174 TYR 0.014 0.001 TYR A 104 ARG 0.002 0.000 ARG A 438 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.447 Fit side-chains REVERT: A 85 MET cc_start: 0.7468 (mmm) cc_final: 0.7050 (mtt) REVERT: A 230 ASP cc_start: 0.8110 (t0) cc_final: 0.7886 (t0) REVERT: A 341 PHE cc_start: 0.8727 (m-10) cc_final: 0.8491 (m-10) REVERT: A 468 GLU cc_start: 0.7863 (mm-30) cc_final: 0.6965 (tm-30) outliers start: 5 outliers final: 5 residues processed: 53 average time/residue: 0.1138 time to fit residues: 8.4738 Evaluate side-chains 54 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 0.0020 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.116283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.089725 restraints weight = 6290.285| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.73 r_work: 0.2890 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4146 Z= 0.168 Angle : 0.519 9.234 5654 Z= 0.248 Chirality : 0.042 0.126 635 Planarity : 0.004 0.039 708 Dihedral : 6.049 45.684 594 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.20 % Allowed : 14.42 % Favored : 84.38 % 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: 1.08 (0.39), residues: 508 helix: 2.08 (0.33), residues: 254 sheet: -0.81 (0.65), residues: 59 loop : -0.59 (0.48), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 213 HIS 0.001 0.000 HIS A 337 PHE 0.008 0.001 PHE A 174 TYR 0.013 0.001 TYR A 104 ARG 0.002 0.000 ARG A 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1253.44 seconds wall clock time: 23 minutes 3.10 seconds (1383.10 seconds total)