Starting phenix.real_space_refine on Wed Mar 5 21:46:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j76_36029/03_2025/8j76_36029.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j76_36029/03_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_36029/03_2025/8j76_36029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j76_36029/03_2025/8j76_36029.map" model { file = "/net/cci-nas-00/data/ceres_data/8j76_36029/03_2025/8j76_36029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j76_36029/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.23, per 1000 atoms: 0.86 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: 1.14 Conformation dependent library (CDL) restraints added in 479.7 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: 0.99 Time building geometry restraints manager: 1.33 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: 0.990 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.510 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.750 ------------------------------------------------------------------------------- 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 : 0.363 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: 0.1388 time to fit residues: 21.3154 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 : 0.446 ------------------------------------------------------------------------------- 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 = 48)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.175042 restraints weight = 6896.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.178609 restraints weight = 3722.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.180984 restraints weight = 2344.699| |-----------------------------------------------------------------------------| 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 : 0.414 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 101 average time/residue: 0.1165 time to fit residues: 15.5736 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 : 0.391 ------------------------------------------------------------------------------- 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: 0.9990 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: 1.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 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 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.188857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.174597 restraints weight = 6902.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.178078 restraints weight = 3764.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.180419 restraints weight = 2375.444| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2024 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= 0.204 Angle : 0.692 9.790 5294 Z= 0.347 Chirality : 0.046 0.374 626 Planarity : 0.005 0.036 642 Dihedral : 8.165 59.084 590 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.26 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: -0.50 (0.38), residues: 487 helix: 0.74 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -2.66 (0.46), residues: 159 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 0.012 0.001 PHE A 334 TYR 0.017 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 : 0.394 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 91 average time/residue: 0.1338 time to fit residues: 15.8161 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 : 0.403 ------------------------------------------------------------------------------- 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: 0.8980 chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.190032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.176545 restraints weight = 6835.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.180062 restraints weight = 3692.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.182354 restraints weight = 2287.838| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3874 Z= 0.199 Angle : 0.666 9.945 5294 Z= 0.332 Chirality : 0.045 0.351 626 Planarity : 0.005 0.036 642 Dihedral : 7.445 59.740 590 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % 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: -0.33 (0.38), residues: 487 helix: 0.84 (0.28), residues: 328 sheet: None (None), residues: 0 loop : -2.53 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 254 HIS 0.003 0.001 HIS A 4 PHE 0.011 0.001 PHE A 479 TYR 0.016 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 105 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.388 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 96 average time/residue: 0.1139 time to fit residues: 14.4374 Evaluate side-chains 92 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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: 5.9990 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 11 optimal weight: 0.0570 chunk 22 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.192323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.178519 restraints weight = 7082.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.181974 restraints weight = 3890.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.184225 restraints weight = 2445.802| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2525 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= 0.174 Angle : 0.653 9.849 5294 Z= 0.325 Chirality : 0.044 0.353 626 Planarity : 0.005 0.035 642 Dihedral : 7.271 59.784 590 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.77 % Allowed : 22.55 % 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: -0.13 (0.38), residues: 487 helix: 0.99 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -2.47 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 62 HIS 0.002 0.001 HIS A 4 PHE 0.012 0.001 PHE A 479 TYR 0.022 0.001 TYR A 414 ARG 0.001 0.000 ARG A 446 *********************** 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 104 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.411 Fit side-chains REVERT: A 480 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7336 (mttt) outliers start: 18 outliers final: 8 residues processed: 95 average time/residue: 0.1142 time to fit residues: 14.3257 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 : 0.364 ------------------------------------------------------------------------------- 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 275 PHE 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: 0.7980 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 13 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4203 r_free = 0.4203 target = 0.191313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.177821 restraints weight = 6870.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.181205 restraints weight = 3726.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.183530 restraints weight = 2319.748| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2689 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= 0.191 Angle : 0.666 9.892 5294 Z= 0.331 Chirality : 0.044 0.352 626 Planarity : 0.005 0.041 642 Dihedral : 7.189 59.286 590 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.24 % Allowed : 23.34 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.38), residues: 487 helix: 1.03 (0.28), residues: 327 sheet: None (None), residues: 0 loop : -2.37 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 62 HIS 0.002 0.001 HIS A 4 PHE 0.012 0.001 PHE A 479 TYR 0.030 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 102 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.437 Fit side-chains REVERT: A 248 MET cc_start: 0.8793 (tmt) cc_final: 0.7839 (tmt) REVERT: A 480 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7354 (mttt) outliers start: 16 outliers final: 10 residues processed: 95 average time/residue: 0.1156 time to fit residues: 14.6198 Evaluate side-chains 90 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 268 THR Chi-restraints excluded: chain A residue 275 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 0.0670 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 = 0.4163 r_free = 0.4163 target = 0.188415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.173862 restraints weight = 7115.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.177297 restraints weight = 3933.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.179619 restraints weight = 2501.403| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3874 Z= 0.201 Angle : 0.697 12.066 5294 Z= 0.340 Chirality : 0.044 0.352 626 Planarity : 0.005 0.039 642 Dihedral : 7.186 58.891 590 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.51 % Allowed : 24.14 % Favored : 71.35 % 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: 0.10 (0.38), residues: 487 helix: 1.07 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -2.16 (0.49), 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 0.011 0.001 PHE A 479 TYR 0.022 0.001 TYR A 414 ARG 0.001 0.000 ARG A 260 *********************** 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 to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.361 Fit side-chains REVERT: A 440 VAL cc_start: 0.6783 (m) cc_final: 0.6474 (m) REVERT: A 480 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7345 (mttt) outliers start: 17 outliers final: 11 residues processed: 93 average time/residue: 0.1070 time to fit residues: 13.3088 Evaluate side-chains 95 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.187019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.172703 restraints weight = 6953.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.176239 restraints weight = 3734.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.178625 restraints weight = 2325.998| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2971 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= 0.202 Angle : 0.695 10.206 5294 Z= 0.340 Chirality : 0.044 0.351 626 Planarity : 0.005 0.038 642 Dihedral : 7.182 59.459 590 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.98 % Allowed : 25.73 % 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: 0.15 (0.38), residues: 487 helix: 1.10 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -2.10 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 62 HIS 0.003 0.001 HIS A 4 PHE 0.012 0.001 PHE A 479 TYR 0.024 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 to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.420 Fit side-chains REVERT: A 480 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7334 (mttt) outliers start: 15 outliers final: 12 residues processed: 95 average time/residue: 0.1124 time to fit residues: 14.2272 Evaluate side-chains 97 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 0.0040 chunk 38 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 0.0010 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.0870 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.3376 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.190261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.176091 restraints weight = 6811.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.179590 restraints weight = 3659.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.181939 restraints weight = 2276.675| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.3219 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= 0.176 Angle : 0.683 9.745 5294 Z= 0.331 Chirality : 0.044 0.347 626 Planarity : 0.004 0.036 642 Dihedral : 7.139 59.959 590 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.45 % Allowed : 28.12 % 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: 0.28 (0.38), residues: 487 helix: 1.23 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -2.11 (0.50), residues: 158 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 0.024 0.001 TYR A 122 ARG 0.002 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 97 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.393 Fit side-chains REVERT: A 121 ILE cc_start: 0.7969 (mt) cc_final: 0.7675 (tt) REVERT: A 158 ASP cc_start: 0.8247 (t70) cc_final: 0.7837 (t70) REVERT: A 330 VAL cc_start: 0.7988 (m) cc_final: 0.7772 (p) REVERT: A 440 VAL cc_start: 0.6846 (m) cc_final: 0.6562 (m) REVERT: A 480 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7182 (mttm) outliers start: 13 outliers final: 10 residues processed: 92 average time/residue: 0.1168 time to fit residues: 14.2154 Evaluate side-chains 91 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 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 249 LEU Chi-restraints excluded: chain A residue 268 THR 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 28 optimal weight: 0.8980 chunk 40 optimal weight: 0.0060 chunk 16 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.189827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.175297 restraints weight = 7084.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.178712 restraints weight = 3941.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.180979 restraints weight = 2511.741| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.3283 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= 0.186 Angle : 0.686 9.863 5294 Z= 0.335 Chirality : 0.044 0.349 626 Planarity : 0.005 0.040 642 Dihedral : 7.068 59.501 590 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.18 % Allowed : 28.65 % 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: 0.33 (0.39), residues: 487 helix: 1.24 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -2.07 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 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 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 96 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.366 Fit side-chains REVERT: A 121 ILE cc_start: 0.7785 (mt) cc_final: 0.7516 (tt) REVERT: A 158 ASP cc_start: 0.8259 (t70) cc_final: 0.7846 (t70) REVERT: A 330 VAL cc_start: 0.8000 (m) cc_final: 0.7787 (p) REVERT: A 480 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7349 (mttt) outliers start: 12 outliers final: 9 residues processed: 91 average time/residue: 0.1087 time to fit residues: 13.3180 Evaluate side-chains 91 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.188924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.174423 restraints weight = 6948.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.177806 restraints weight = 3887.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.180045 restraints weight = 2487.059| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3328 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= 0.203 Angle : 0.700 9.873 5294 Z= 0.342 Chirality : 0.044 0.343 626 Planarity : 0.005 0.035 642 Dihedral : 7.091 58.034 590 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.18 % Allowed : 29.18 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.38), residues: 487 helix: 1.33 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -1.92 (0.49), residues: 161 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 0.027 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: 1447.82 seconds wall clock time: 25 minutes 45.19 seconds (1545.19 seconds total)