Starting phenix.real_space_refine on Tue Feb 11 02:39:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j76_36029/02_2025/8j76_36029.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j76_36029/02_2025/8j76_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/cci-nas-00/data/ceres_data/8j76_36029/02_2025/8j76_36029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j76_36029/02_2025/8j76_36029.map" model { file = "/net/cci-nas-00/data/ceres_data/8j76_36029/02_2025/8j76_36029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j76_36029/02_2025/8j76_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 3.22, per 1000 atoms: 0.85 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: 1.89 Conformation dependent library (CDL) restraints added in 492.8 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: 0.34 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: 0.94 Time building geometry restraints manager: 1.55 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: 0.710 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.380 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.090 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.396 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: 0.1315 time to fit residues: 20.2798 Evaluate side-chains 100 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.189472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.175037 restraints weight = 6896.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.178583 restraints weight = 3726.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.180942 restraints weight = 2350.528| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 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 to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.398 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 101 average time/residue: 0.1189 time to fit residues: 15.8719 Evaluate side-chains 93 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 32 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.188656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.174386 restraints weight = 6903.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.177877 restraints weight = 3751.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.180212 restraints weight = 2373.070| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.1989 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= 0.205 Angle : 0.695 9.824 5294 Z= 0.349 Chirality : 0.046 0.376 626 Planarity : 0.005 0.036 642 Dihedral : 8.316 59.234 590 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % 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: -0.51 (0.38), residues: 487 helix: 0.73 (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 0.013 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 98 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.419 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 91 average time/residue: 0.1261 time to fit residues: 15.0251 Evaluate side-chains 88 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 45 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.190379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.176937 restraints weight = 6864.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.180397 restraints weight = 3714.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.182716 restraints weight = 2300.806| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2300 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= 0.194 Angle : 0.669 9.951 5294 Z= 0.333 Chirality : 0.044 0.352 626 Planarity : 0.005 0.036 642 Dihedral : 7.500 59.856 590 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.24 % Allowed : 20.42 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.36 (0.38), residues: 487 helix: 0.82 (0.28), residues: 328 sheet: None (None), residues: 0 loop : -2.56 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 62 HIS 0.003 0.001 HIS A 4 PHE 0.011 0.001 PHE A 479 TYR 0.017 0.001 TYR A 111 ARG 0.001 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 103 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.436 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 95 average time/residue: 0.1200 time to fit residues: 15.3175 Evaluate side-chains 90 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 248 MET Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 282 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.4174 r_free = 0.4174 target = 0.188435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.175122 restraints weight = 6992.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.178557 restraints weight = 3745.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.180897 restraints weight = 2312.514| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2446 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= 0.220 Angle : 0.704 10.360 5294 Z= 0.349 Chirality : 0.045 0.358 626 Planarity : 0.005 0.036 642 Dihedral : 7.373 59.553 590 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.04 % Allowed : 22.28 % Favored : 72.68 % 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: -0.23 (0.38), residues: 487 helix: 0.91 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -2.49 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 62 HIS 0.003 0.001 HIS A 4 PHE 0.013 0.001 PHE A 426 TYR 0.022 0.002 TYR A 186 ARG 0.002 0.000 ARG A 107 *********************** 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 105 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.406 Fit side-chains REVERT: A 331 TYR cc_start: 0.7172 (p90) cc_final: 0.6967 (p90) REVERT: A 480 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7255 (mttt) outliers start: 19 outliers final: 11 residues processed: 96 average time/residue: 0.1193 time to fit residues: 15.0611 Evaluate side-chains 97 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 214 ASP Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 282 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 0.0980 chunk 3 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.190825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.177500 restraints weight = 6838.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.181014 restraints weight = 3669.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.183197 restraints weight = 2256.940| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2686 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= 0.189 Angle : 0.682 9.860 5294 Z= 0.336 Chirality : 0.044 0.353 626 Planarity : 0.005 0.037 642 Dihedral : 7.306 59.522 590 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.77 % Allowed : 24.14 % 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: -0.11 (0.38), residues: 487 helix: 1.00 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -2.39 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 62 HIS 0.002 0.001 HIS A 4 PHE 0.011 0.001 PHE A 479 TYR 0.029 0.001 TYR A 414 ARG 0.001 0.000 ARG A 369 *********************** 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 107 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.457 Fit side-chains REVERT: A 440 VAL cc_start: 0.6745 (m) cc_final: 0.6418 (m) REVERT: A 480 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7320 (mttt) outliers start: 18 outliers final: 9 residues processed: 98 average time/residue: 0.1165 time to fit residues: 15.2658 Evaluate side-chains 92 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 268 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 16 optimal weight: 0.0670 chunk 20 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.193107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.179186 restraints weight = 6987.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.182593 restraints weight = 3834.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.184851 restraints weight = 2427.338| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2908 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= 0.179 Angle : 0.683 9.808 5294 Z= 0.335 Chirality : 0.044 0.351 626 Planarity : 0.005 0.042 642 Dihedral : 7.233 59.881 590 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.24 % Allowed : 25.46 % Favored : 70.29 % 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: 0.13 (0.38), residues: 487 helix: 1.12 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -2.20 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 62 HIS 0.002 0.001 HIS A 4 PHE 0.014 0.001 PHE A 102 TYR 0.024 0.001 TYR A 414 ARG 0.001 0.000 ARG A 107 *********************** 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 101 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.415 Fit side-chains REVERT: A 440 VAL cc_start: 0.6774 (m) cc_final: 0.6454 (m) REVERT: A 480 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7391 (mttt) outliers start: 16 outliers final: 10 residues processed: 93 average time/residue: 0.1150 time to fit residues: 14.2232 Evaluate side-chains 92 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 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 38 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 43 optimal weight: 0.0270 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.193375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.179234 restraints weight = 7015.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.182783 restraints weight = 3799.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.185073 restraints weight = 2376.434| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3092 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= 0.180 Angle : 0.689 9.829 5294 Z= 0.337 Chirality : 0.044 0.352 626 Planarity : 0.004 0.038 642 Dihedral : 7.181 59.284 590 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.98 % Allowed : 25.99 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.23 (0.38), residues: 487 helix: 1.18 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -2.14 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 62 HIS 0.002 0.001 HIS A 4 PHE 0.011 0.001 PHE A 102 TYR 0.025 0.001 TYR A 122 ARG 0.001 0.000 ARG A 369 *********************** 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 102 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.377 Fit side-chains REVERT: A 121 ILE cc_start: 0.8062 (mt) cc_final: 0.7757 (tt) REVERT: A 440 VAL cc_start: 0.6851 (m) cc_final: 0.6534 (m) REVERT: A 480 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7215 (mttm) outliers start: 15 outliers final: 11 residues processed: 93 average time/residue: 0.1187 time to fit residues: 14.4332 Evaluate side-chains 96 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 0.0470 chunk 38 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.8680 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.187882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.173688 restraints weight = 6807.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.177152 restraints weight = 3683.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.179436 restraints weight = 2296.487| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3190 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= 0.201 Angle : 0.697 9.882 5294 Z= 0.342 Chirality : 0.045 0.354 626 Planarity : 0.005 0.038 642 Dihedral : 7.229 59.092 590 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.24 % Allowed : 27.32 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.26 (0.39), residues: 487 helix: 1.20 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -2.12 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 62 HIS 0.003 0.001 HIS A 4 PHE 0.015 0.001 PHE A 102 TYR 0.026 0.001 TYR A 122 ARG 0.001 0.000 ARG A 107 *********************** 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 100 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.432 Fit side-chains REVERT: A 121 ILE cc_start: 0.7961 (mt) cc_final: 0.7678 (tt) REVERT: A 440 VAL cc_start: 0.6904 (m) cc_final: 0.6608 (m) REVERT: A 480 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7230 (mttm) outliers start: 16 outliers final: 12 residues processed: 93 average time/residue: 0.1120 time to fit residues: 13.8994 Evaluate side-chains 99 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP 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 268 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 358 MET 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 28 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.188056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.173857 restraints weight = 6928.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.177349 restraints weight = 3722.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.179652 restraints weight = 2311.712| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3293 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= 0.201 Angle : 0.698 9.862 5294 Z= 0.344 Chirality : 0.045 0.351 626 Planarity : 0.005 0.040 642 Dihedral : 7.284 58.194 590 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.71 % Allowed : 27.85 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 1.20 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -2.00 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 62 HIS 0.003 0.001 HIS A 4 PHE 0.012 0.001 PHE A 479 TYR 0.029 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 98 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.411 Fit side-chains REVERT: A 121 ILE cc_start: 0.7786 (mt) cc_final: 0.7555 (tt) REVERT: A 158 ASP cc_start: 0.8264 (t70) cc_final: 0.7906 (t70) REVERT: A 480 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7252 (mttm) outliers start: 14 outliers final: 13 residues processed: 91 average time/residue: 0.1165 time to fit residues: 14.0932 Evaluate side-chains 97 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP 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 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 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4146 r_free = 0.4146 target = 0.187131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.172887 restraints weight = 6812.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.176320 restraints weight = 3700.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.178585 restraints weight = 2321.116| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3874 Z= 0.210 Angle : 0.702 9.898 5294 Z= 0.345 Chirality : 0.045 0.351 626 Planarity : 0.005 0.039 642 Dihedral : 7.197 57.051 590 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.98 % Allowed : 28.12 % Favored : 67.90 % 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: 0.43 (0.39), residues: 487 helix: 1.30 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -1.88 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 62 HIS 0.003 0.001 HIS A 4 PHE 0.011 0.001 PHE A 479 TYR 0.028 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: 1423.22 seconds wall clock time: 26 minutes 14.90 seconds (1574.90 seconds total)