Starting phenix.real_space_refine on Mon Sep 23 16:07:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j76_36029/09_2024/8j76_36029.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j76_36029/09_2024/8j76_36029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j76_36029/09_2024/8j76_36029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j76_36029/09_2024/8j76_36029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j76_36029/09_2024/8j76_36029.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j76_36029/09_2024/8j76_36029.cif" } resolution = 3.7 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= 0.106 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 19 5.16 5 C 2508 2.51 5 N 576 2.21 5 O 668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3771 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3732 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 22, 'TRANS': 470} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 2, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.71, per 1000 atoms: 1.25 Number of scatterers: 3771 At special positions: 0 Unit cell: (86.1, 70.52, 91.02, 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 19 16.00 O 668 8.00 N 576 7.00 C 2508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A 301 " Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 627.2 milliseconds 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 898 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 75.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 3 through 28 removed outlier: 3.805A pdb=" N GLY A 7 " --> pdb=" O PHE A 3 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG A 28 " --> pdb=" O TRP A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 63 removed outlier: 4.026A pdb=" N VAL A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TRP A 62 " --> pdb=" O MET A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 removed outlier: 4.218A pdb=" N ASN A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 84 Processing helix chain 'A' and resid 85 through 103 removed outlier: 3.979A pdb=" N ILE A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.056A pdb=" N ARG A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.167A pdb=" N PHE A 118 " --> pdb=" O MET A 114 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 157 removed outlier: 4.032A pdb=" N LEU A 129 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 161 through 178 removed outlier: 3.646A pdb=" N VAL A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 207 removed outlier: 4.006A pdb=" N LEU A 192 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.670A pdb=" N THR A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 251 Processing helix chain 'A' and resid 254 through 263 removed outlier: 3.826A pdb=" N PHE A 258 " --> pdb=" O TRP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 298 removed outlier: 3.658A pdb=" N ALA A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Proline residue: A 287 - end of helix removed outlier: 3.572A pdb=" N LEU A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 329 through 367 removed outlier: 4.035A pdb=" N PHE A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 399 removed outlier: 3.862A pdb=" N LEU A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 426 removed outlier: 4.481A pdb=" N PHE A 418 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 431 through 448 Processing helix chain 'A' and resid 479 through 501 247 hydrogen bonds defined for protein. 738 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: 0.95 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 568 1.29 - 1.42: 1066 1.42 - 1.55: 2200 1.55 - 1.68: 6 1.68 - 1.81: 34 Bond restraints: 3874 Sorted by residual: bond pdb=" CA ILE A 252 " pdb=" C ILE A 252 " ideal model delta sigma weight residual 1.523 1.444 0.079 9.20e-03 1.18e+04 7.40e+01 bond pdb=" C ILE A 252 " pdb=" O ILE A 252 " ideal model delta sigma weight residual 1.242 1.179 0.063 8.60e-03 1.35e+04 5.30e+01 bond pdb=" C TYR A 91 " pdb=" O TYR A 91 " ideal model delta sigma weight residual 1.237 1.154 0.082 1.16e-02 7.43e+03 5.02e+01 bond pdb=" N TYR A 91 " pdb=" CA TYR A 91 " ideal model delta sigma weight residual 1.459 1.380 0.080 1.20e-02 6.94e+03 4.41e+01 bond pdb=" CA PRO A 253 " pdb=" C PRO A 253 " ideal model delta sigma weight residual 1.517 1.422 0.095 1.46e-02 4.69e+03 4.21e+01 ... (remaining 3869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.38: 5260 5.38 - 10.77: 27 10.77 - 16.15: 2 16.15 - 21.53: 3 21.53 - 26.92: 2 Bond angle restraints: 5294 Sorted by residual: angle pdb=" N ASP A 469 " pdb=" CA ASP A 469 " pdb=" C ASP A 469 " ideal model delta sigma weight residual 114.16 89.53 24.63 1.48e+00 4.57e-01 2.77e+02 angle pdb=" N GLN A 255 " pdb=" CA GLN A 255 " pdb=" C GLN A 255 " ideal model delta sigma weight residual 111.33 130.05 -18.72 1.21e+00 6.83e-01 2.39e+02 angle pdb=" N GLU A 503 " pdb=" CA GLU A 503 " pdb=" C GLU A 503 " ideal model delta sigma weight residual 110.33 129.19 -18.86 1.29e+00 6.01e-01 2.14e+02 angle pdb=" N ASP A 468 " pdb=" CA ASP A 468 " pdb=" C ASP A 468 " ideal model delta sigma weight residual 110.80 137.72 -26.92 2.13e+00 2.20e-01 1.60e+02 angle pdb=" N ASP A 469 " pdb=" CA ASP A 469 " pdb=" CB ASP A 469 " ideal model delta sigma weight residual 110.88 130.68 -19.80 1.88e+00 2.83e-01 1.11e+02 ... (remaining 5289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 2086 21.89 - 43.78: 124 43.78 - 65.67: 11 65.67 - 87.56: 9 87.56 - 109.46: 4 Dihedral angle restraints: 2234 sinusoidal: 818 harmonic: 1416 Sorted by residual: dihedral pdb=" N ASP A 468 " pdb=" C ASP A 468 " pdb=" CA ASP A 468 " pdb=" CB ASP A 468 " ideal model delta harmonic sigma weight residual 122.80 153.22 -30.42 0 2.50e+00 1.60e-01 1.48e+02 dihedral pdb=" C ASP A 468 " pdb=" N ASP A 468 " pdb=" CA ASP A 468 " pdb=" CB ASP A 468 " ideal model delta harmonic sigma weight residual -122.60 -150.72 28.12 0 2.50e+00 1.60e-01 1.27e+02 dihedral pdb=" C TYR A 364 " pdb=" N TYR A 364 " pdb=" CA TYR A 364 " pdb=" CB TYR A 364 " ideal model delta harmonic sigma weight residual -122.60 -136.60 14.00 0 2.50e+00 1.60e-01 3.14e+01 ... (remaining 2231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.294: 618 0.294 - 0.588: 5 0.588 - 0.882: 2 0.882 - 1.175: 0 1.175 - 1.469: 1 Chirality restraints: 626 Sorted by residual: chirality pdb=" CA ASP A 468 " pdb=" N ASP A 468 " pdb=" C ASP A 468 " pdb=" CB ASP A 468 " both_signs ideal model delta sigma weight residual False 2.51 1.04 1.47 2.00e-01 2.50e+01 5.40e+01 chirality pdb=" CA PRO A 253 " pdb=" N PRO A 253 " pdb=" C PRO A 253 " pdb=" CB PRO A 253 " both_signs ideal model delta sigma weight residual False 2.72 1.98 0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 301 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.19e+01 ... (remaining 623 not shown) Planarity restraints: 643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 251 " 0.019 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C GLY A 251 " -0.062 2.00e-02 2.50e+03 pdb=" O GLY A 251 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE A 252 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 467 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C PRO A 467 " 0.060 2.00e-02 2.50e+03 pdb=" O PRO A 467 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP A 468 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 254 " 0.012 2.00e-02 2.50e+03 2.42e-02 5.85e+00 pdb=" C TRP A 254 " -0.042 2.00e-02 2.50e+03 pdb=" O TRP A 254 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN A 255 " 0.014 2.00e-02 2.50e+03 ... (remaining 640 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 18 2.52 - 3.12: 3125 3.12 - 3.71: 5795 3.71 - 4.31: 7648 4.31 - 4.90: 12708 Nonbonded interactions: 29294 Sorted by model distance: nonbonded pdb=" O ASP A 468 " pdb=" OD1 ASP A 468 " model vdw 1.926 3.040 nonbonded pdb=" C ASP A 468 " pdb=" OD1 ASP A 468 " model vdw 2.079 3.270 nonbonded pdb=" N ASP A 469 " pdb=" N ASN A 470 " model vdw 2.182 2.560 nonbonded pdb=" OG1 THR A 218 " pdb=" OG SER A 297 " model vdw 2.211 3.040 nonbonded pdb=" OE1 GLN A 86 " pdb=" NE1 TRP A 240 " model vdw 2.300 3.120 ... (remaining 29289 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.770 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 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 : 0.007 0.096 3874 Z= 0.442 Angle : 1.236 26.915 5294 Z= 0.749 Chirality : 0.095 1.469 626 Planarity : 0.005 0.039 642 Dihedral : 15.608 109.455 1336 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.27 % Allowed : 0.80 % Favored : 98.94 % Cbeta Deviations : 0.89 % 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: -1.36 (0.37), residues: 487 helix: 0.14 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -2.87 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 62 HIS 0.003 0.001 HIS A 4 PHE 0.022 0.002 PHE A 334 TYR 0.020 0.002 TYR A 111 ARG 0.002 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 0.368 Fit side-chains REVERT: A 249 LEU cc_start: 0.8260 (mp) cc_final: 0.8057 (mp) REVERT: A 484 MET cc_start: 0.8614 (tmm) cc_final: 0.8362 (tmm) outliers start: 1 outliers final: 1 residues processed: 122 average time/residue: 0.1376 time to fit residues: 21.0551 Evaluate side-chains 100 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.0270 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 0.1980 chunk 19 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3874 Z= 0.214 Angle : 0.744 9.923 5294 Z= 0.377 Chirality : 0.047 0.400 626 Planarity : 0.005 0.047 642 Dihedral : 10.534 65.258 590 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.16 % Favored : 93.63 % Rotamer: Outliers : 2.65 % Allowed : 12.20 % Favored : 85.15 % 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: -0.79 (0.38), residues: 487 helix: 0.53 (0.28), residues: 328 sheet: None (None), residues: 0 loop : -2.81 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 254 HIS 0.003 0.001 HIS A 162 PHE 0.013 0.001 PHE A 477 TYR 0.015 0.001 TYR A 111 ARG 0.003 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.396 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 101 average time/residue: 0.1135 time to fit residues: 15.1451 Evaluate side-chains 93 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 406 TRP Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 33 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3874 Z= 0.195 Angle : 0.687 9.767 5294 Z= 0.345 Chirality : 0.046 0.376 626 Planarity : 0.005 0.036 642 Dihedral : 8.303 59.099 590 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.65 % Allowed : 19.10 % Favored : 78.25 % 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: -0.48 (0.38), residues: 487 helix: 0.76 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -2.68 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 254 HIS 0.003 0.001 HIS A 162 PHE 0.012 0.001 PHE A 334 TYR 0.016 0.001 TYR A 331 ARG 0.002 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.340 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 0.1248 time to fit residues: 14.8921 Evaluate side-chains 88 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 406 TRP Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.0070 chunk 42 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3874 Z= 0.178 Angle : 0.659 9.912 5294 Z= 0.328 Chirality : 0.044 0.350 626 Planarity : 0.005 0.039 642 Dihedral : 7.421 59.581 590 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.51 % Allowed : 19.89 % Favored : 75.60 % 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: -0.31 (0.38), residues: 487 helix: 0.87 (0.28), residues: 328 sheet: None (None), residues: 0 loop : -2.54 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 62 HIS 0.002 0.001 HIS A 4 PHE 0.012 0.001 PHE A 479 TYR 0.015 0.001 TYR A 111 ARG 0.002 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 0.396 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 97 average time/residue: 0.1114 time to fit residues: 14.5685 Evaluate side-chains 91 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 406 TRP Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3874 Z= 0.278 Angle : 0.739 10.110 5294 Z= 0.372 Chirality : 0.047 0.362 626 Planarity : 0.005 0.037 642 Dihedral : 7.421 58.583 590 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.24 % Allowed : 23.61 % Favored : 72.15 % 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: -0.40 (0.38), residues: 487 helix: 0.71 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -2.44 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 62 HIS 0.005 0.002 HIS A 4 PHE 0.019 0.002 PHE A 426 TYR 0.020 0.002 TYR A 186 ARG 0.001 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 0.397 Fit side-chains REVERT: A 62 TRP cc_start: 0.7108 (m-10) cc_final: 0.6798 (m-10) REVERT: A 406 TRP cc_start: 0.8768 (OUTLIER) cc_final: 0.8430 (t60) REVERT: A 480 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7462 (mttt) outliers start: 16 outliers final: 8 residues processed: 97 average time/residue: 0.0999 time to fit residues: 12.9490 Evaluate side-chains 95 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 406 TRP Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 480 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.0870 chunk 47 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 0.0470 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3874 Z= 0.180 Angle : 0.666 9.782 5294 Z= 0.332 Chirality : 0.044 0.351 626 Planarity : 0.005 0.037 642 Dihedral : 7.301 57.485 590 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.71 % Allowed : 24.40 % Favored : 71.88 % 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: -0.11 (0.38), residues: 487 helix: 0.94 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -2.32 (0.48), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 254 HIS 0.002 0.001 HIS A 4 PHE 0.011 0.001 PHE A 479 TYR 0.020 0.001 TYR A 122 ARG 0.002 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.408 Fit side-chains REVERT: A 62 TRP cc_start: 0.7010 (m-10) cc_final: 0.6767 (m-10) REVERT: A 406 TRP cc_start: 0.8515 (OUTLIER) cc_final: 0.8266 (t60) REVERT: A 440 VAL cc_start: 0.6837 (m) cc_final: 0.6508 (m) REVERT: A 480 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7344 (mttt) outliers start: 14 outliers final: 5 residues processed: 93 average time/residue: 0.1198 time to fit residues: 14.6899 Evaluate side-chains 88 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 406 TRP Chi-restraints excluded: chain A residue 480 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3874 Z= 0.196 Angle : 0.708 11.758 5294 Z= 0.343 Chirality : 0.045 0.353 626 Planarity : 0.005 0.037 642 Dihedral : 7.249 59.639 590 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.24 % Allowed : 24.67 % Favored : 71.09 % 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: -0.04 (0.38), residues: 487 helix: 0.97 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -2.22 (0.48), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 62 HIS 0.003 0.001 HIS A 4 PHE 0.009 0.001 PHE A 426 TYR 0.023 0.001 TYR A 122 ARG 0.001 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.399 Fit side-chains REVERT: A 248 MET cc_start: 0.8696 (tmt) cc_final: 0.7808 (tmt) REVERT: A 480 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7405 (mttt) outliers start: 16 outliers final: 11 residues processed: 92 average time/residue: 0.1126 time to fit residues: 13.7524 Evaluate side-chains 91 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 406 TRP Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 480 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3874 Z= 0.208 Angle : 0.731 10.351 5294 Z= 0.351 Chirality : 0.046 0.356 626 Planarity : 0.005 0.036 642 Dihedral : 7.215 58.631 590 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.24 % Allowed : 25.20 % Favored : 70.56 % 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: 0.06 (0.38), residues: 487 helix: 1.03 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -2.14 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 62 HIS 0.003 0.001 HIS A 4 PHE 0.009 0.001 PHE A 426 TYR 0.025 0.001 TYR A 122 ARG 0.001 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.392 Fit side-chains REVERT: A 248 MET cc_start: 0.8742 (tmt) cc_final: 0.7898 (tmt) REVERT: A 480 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7433 (mttt) outliers start: 16 outliers final: 11 residues processed: 92 average time/residue: 0.1138 time to fit residues: 13.9535 Evaluate side-chains 96 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 406 TRP Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 480 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.0670 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 0.1980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3874 Z= 0.183 Angle : 0.710 9.801 5294 Z= 0.339 Chirality : 0.045 0.351 626 Planarity : 0.004 0.037 642 Dihedral : 7.179 57.443 590 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.18 % Allowed : 26.79 % Favored : 70.03 % 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: 0.20 (0.38), residues: 487 helix: 1.17 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -2.18 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 62 HIS 0.002 0.001 HIS A 4 PHE 0.011 0.001 PHE A 479 TYR 0.026 0.001 TYR A 122 ARG 0.001 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.396 Fit side-chains REVERT: A 121 ILE cc_start: 0.7939 (mt) cc_final: 0.7655 (tt) REVERT: A 248 MET cc_start: 0.8728 (tmt) cc_final: 0.7886 (tmt) REVERT: A 440 VAL cc_start: 0.6839 (m) cc_final: 0.6518 (m) REVERT: A 480 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7529 (mttt) outliers start: 12 outliers final: 10 residues processed: 92 average time/residue: 0.1105 time to fit residues: 13.5201 Evaluate side-chains 96 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 406 TRP Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 480 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 11 optimal weight: 0.0000 chunk 35 optimal weight: 0.2980 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3874 Z= 0.183 Angle : 0.710 9.817 5294 Z= 0.341 Chirality : 0.045 0.351 626 Planarity : 0.004 0.038 642 Dihedral : 7.095 57.054 590 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.24 % Allowed : 27.59 % Favored : 68.17 % 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: 0.25 (0.39), residues: 487 helix: 1.23 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -2.22 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 62 HIS 0.002 0.001 HIS A 4 PHE 0.011 0.001 PHE A 479 TYR 0.027 0.001 TYR A 122 ARG 0.001 0.000 ARG A 369 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.392 Fit side-chains REVERT: A 121 ILE cc_start: 0.7719 (mt) cc_final: 0.7502 (tt) REVERT: A 248 MET cc_start: 0.8862 (tmt) cc_final: 0.8067 (tmt) REVERT: A 440 VAL cc_start: 0.6864 (m) cc_final: 0.6545 (m) REVERT: A 480 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7556 (mttt) outliers start: 16 outliers final: 11 residues processed: 93 average time/residue: 0.1157 time to fit residues: 14.2098 Evaluate side-chains 93 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 406 TRP Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 480 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 0.0270 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.0770 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.189675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.175560 restraints weight = 6849.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.179065 restraints weight = 3682.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.181381 restraints weight = 2282.398| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3874 Z= 0.182 Angle : 0.705 9.785 5294 Z= 0.338 Chirality : 0.045 0.347 626 Planarity : 0.004 0.038 642 Dihedral : 7.034 56.012 590 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.18 % Allowed : 28.38 % Favored : 68.44 % 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: 0.43 (0.39), residues: 487 helix: 1.37 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -2.02 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 62 HIS 0.002 0.001 HIS A 4 PHE 0.012 0.001 PHE A 479 TYR 0.026 0.001 TYR A 122 ARG 0.001 0.000 ARG A 369 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1136.57 seconds wall clock time: 20 minutes 46.77 seconds (1246.77 seconds total)